diff --git a/src/qiskit_sphinx_theme/__init__.py b/src/qiskit_sphinx_theme/__init__.py
index f2dbff0b..773a283f 100644
--- a/src/qiskit_sphinx_theme/__init__.py
+++ b/src/qiskit_sphinx_theme/__init__.py
@@ -71,13 +71,25 @@ def activate_themes(app: sphinx.application.Sphinx, config: sphinx.config.Config
     if config.html_theme == "qiskit":
         # We set a low priority so that our Qiskit CSS file overrides Furo.
         app.add_css_file("styles/furo.css", 100)
-        app.add_js_file("scripts/furo.js")
+        app.add_js_file("scripts/qiskit-sphinx-theme.js")
     else:
         # Sphinx 6 stopped including jQuery by default. Our Pytorch theme depend on jQuery,
         # so activate it for our users automatically.
         app.setup_extension("sphinxcontrib.jquery")
 
 
+def remove_furo_js(
+    app: sphinx.application.Sphinx,
+    pagename: str,
+    templatename: str,
+    context: dict,
+    doctree: sphinx.addnodes.document,
+) -> None:
+    context["script_files"] = [
+        js_file for js_file in context["script_files"] if js_file != "_static/scripts/furo.js"
+    ]
+
+
 # See https://www.sphinx-doc.org/en/master/development/theming.html
 def setup(app: sphinx.application.Sphinx) -> dict[str, bool]:
     # Used to generate URL references. Expected to be e.g. `ecosystem/finance`.
@@ -94,7 +106,8 @@ def setup(app: sphinx.application.Sphinx) -> dict[str, bool]:
     app.add_html_theme("qiskit_sphinx_theme", _get_theme_absolute_path("pytorch"))
     app.add_html_theme("qiskit", _get_theme_absolute_path("theme/qiskit-sphinx-theme"))
 
-    app.connect("html-page-context", remove_thebe_if_not_needed)
     app.connect("config-inited", activate_themes)
+    app.connect("html-page-context", remove_furo_js, priority=600)
+    app.connect("html-page-context", remove_thebe_if_not_needed)
 
     return {"parallel_read_safe": True, "parallel_write_safe": True}
diff --git a/src/qiskit_sphinx_theme/assets/scripts/gumshoe-patched.js b/src/qiskit_sphinx_theme/assets/scripts/gumshoe-patched.js
new file mode 100644
index 00000000..0642937e
--- /dev/null
+++ b/src/qiskit_sphinx_theme/assets/scripts/gumshoe-patched.js
@@ -0,0 +1,467 @@
+// Vendored exactly from Furo's `assets/scripts/gumshoe-patched.js`.
+/*!
+ * gumshoejs v5.1.2 (patched by @pradyunsg)
+ * A simple, framework-agnostic scrollspy script.
+ * (c) 2019 Chris Ferdinandi
+ * MIT License
+ * http://github.com/cferdinandi/gumshoe
+ */
+
+(function (root, factory) {
+  if (typeof define === "function" && define.amd) {
+    define([], function () {
+      return factory(root);
+    });
+  } else if (typeof exports === "object") {
+    module.exports = factory(root);
+  } else {
+    root.Gumshoe = factory(root);
+  }
+})(
+  typeof global !== "undefined"
+    ? global
+    : typeof window !== "undefined"
+    ? window
+    : this,
+  function (window) {
+    "use strict";
+
+    //
+    // Defaults
+    //
+
+    var defaults = {
+      // Active classes
+      navClass: "active",
+      contentClass: "active",
+
+      // Nested navigation
+      nested: false,
+      nestedClass: "active",
+
+      // Offset & reflow
+      offset: 0,
+      reflow: false,
+
+      // Event support
+      events: true,
+    };
+
+    //
+    // Methods
+    //
+
+    /**
+     * Merge two or more objects together.
+     * @param   {Object}   objects  The objects to merge together
+     * @returns {Object}            Merged values of defaults and options
+     */
+    var extend = function () {
+      var merged = {};
+      Array.prototype.forEach.call(arguments, function (obj) {
+        for (var key in obj) {
+          if (!obj.hasOwnProperty(key)) return;
+          merged[key] = obj[key];
+        }
+      });
+      return merged;
+    };
+
+    /**
+     * Emit a custom event
+     * @param  {String} type   The event type
+     * @param  {Node}   elem   The element to attach the event to
+     * @param  {Object} detail Any details to pass along with the event
+     */
+    var emitEvent = function (type, elem, detail) {
+      // Make sure events are enabled
+      if (!detail.settings.events) return;
+
+      // Create a new event
+      var event = new CustomEvent(type, {
+        bubbles: true,
+        cancelable: true,
+        detail: detail,
+      });
+
+      // Dispatch the event
+      elem.dispatchEvent(event);
+    };
+
+    /**
+     * Get an element's distance from the top of the Document.
+     * @param  {Node} elem The element
+     * @return {Number}    Distance from the top in pixels
+     */
+    var getOffsetTop = function (elem) {
+      var location = 0;
+      if (elem.offsetParent) {
+        while (elem) {
+          location += elem.offsetTop;
+          elem = elem.offsetParent;
+        }
+      }
+      return location >= 0 ? location : 0;
+    };
+
+    /**
+     * Sort content from first to last in the DOM
+     * @param  {Array} contents The content areas
+     */
+    var sortContents = function (contents) {
+      if (contents) {
+        contents.sort(function (item1, item2) {
+          var offset1 = getOffsetTop(item1.content);
+          var offset2 = getOffsetTop(item2.content);
+          if (offset1 < offset2) return -1;
+          return 1;
+        });
+      }
+    };
+
+    /**
+     * Get the offset to use for calculating position
+     * @param  {Object} settings The settings for this instantiation
+     * @return {Float}           The number of pixels to offset the calculations
+     */
+    var getOffset = function (settings) {
+      // if the offset is a function run it
+      if (typeof settings.offset === "function") {
+        return parseFloat(settings.offset());
+      }
+
+      // Otherwise, return it as-is
+      return parseFloat(settings.offset);
+    };
+
+    /**
+     * Get the document element's height
+     * @private
+     * @returns {Number}
+     */
+    var getDocumentHeight = function () {
+      return Math.max(
+        document.body.scrollHeight,
+        document.documentElement.scrollHeight,
+        document.body.offsetHeight,
+        document.documentElement.offsetHeight,
+        document.body.clientHeight,
+        document.documentElement.clientHeight,
+      );
+    };
+
+    /**
+     * Determine if an element is in view
+     * @param  {Node}    elem     The element
+     * @param  {Object}  settings The settings for this instantiation
+     * @param  {Boolean} bottom   If true, check if element is above bottom of viewport instead
+     * @return {Boolean}          Returns true if element is in the viewport
+     */
+    var isInView = function (elem, settings, bottom) {
+      var bounds = elem.getBoundingClientRect();
+      var offset = getOffset(settings);
+      if (bottom) {
+        return (
+          parseInt(bounds.bottom, 10) <
+          (window.innerHeight || document.documentElement.clientHeight)
+        );
+      }
+      return parseInt(bounds.top, 10) <= offset;
+    };
+
+    /**
+     * Check if at the bottom of the viewport
+     * @return {Boolean} If true, page is at the bottom of the viewport
+     */
+    var isAtBottom = function () {
+      if (
+        Math.ceil(window.innerHeight + window.pageYOffset) >=
+        getDocumentHeight()
+      )
+        return true;
+      return false;
+    };
+
+    /**
+     * Check if the last item should be used (even if not at the top of the page)
+     * @param  {Object} item     The last item
+     * @param  {Object} settings The settings for this instantiation
+     * @return {Boolean}         If true, use the last item
+     */
+    var useLastItem = function (item, settings) {
+      if (isAtBottom() && isInView(item.content, settings, true)) return true;
+      return false;
+    };
+
+    /**
+     * Get the active content
+     * @param  {Array}  contents The content areas
+     * @param  {Object} settings The settings for this instantiation
+     * @return {Object}          The content area and matching navigation link
+     */
+    var getActive = function (contents, settings) {
+      var last = contents[contents.length - 1];
+      if (useLastItem(last, settings)) return last;
+      for (var i = contents.length - 1; i >= 0; i--) {
+        if (isInView(contents[i].content, settings)) return contents[i];
+      }
+    };
+
+    /**
+     * Deactivate parent navs in a nested navigation
+     * @param  {Node}   nav      The starting navigation element
+     * @param  {Object} settings The settings for this instantiation
+     */
+    var deactivateNested = function (nav, settings) {
+      // If nesting isn't activated, bail
+      if (!settings.nested || !nav.parentNode) return;
+
+      // Get the parent navigation
+      var li = nav.parentNode.closest("li");
+      if (!li) return;
+
+      // Remove the active class
+      li.classList.remove(settings.nestedClass);
+
+      // Apply recursively to any parent navigation elements
+      deactivateNested(li, settings);
+    };
+
+    /**
+     * Deactivate a nav and content area
+     * @param  {Object} items    The nav item and content to deactivate
+     * @param  {Object} settings The settings for this instantiation
+     */
+    var deactivate = function (items, settings) {
+      // Make sure there are items to deactivate
+      if (!items) return;
+
+      // Get the parent list item
+      var li = items.nav.closest("li");
+      if (!li) return;
+
+      // Remove the active class from the nav and content
+      li.classList.remove(settings.navClass);
+      items.content.classList.remove(settings.contentClass);
+
+      // Deactivate any parent navs in a nested navigation
+      deactivateNested(li, settings);
+
+      // Emit a custom event
+      emitEvent("gumshoeDeactivate", li, {
+        link: items.nav,
+        content: items.content,
+        settings: settings,
+      });
+    };
+
+    /**
+     * Activate parent navs in a nested navigation
+     * @param  {Node}   nav      The starting navigation element
+     * @param  {Object} settings The settings for this instantiation
+     */
+    var activateNested = function (nav, settings) {
+      // If nesting isn't activated, bail
+      if (!settings.nested) return;
+
+      // Get the parent navigation
+      var li = nav.parentNode.closest("li");
+      if (!li) return;
+
+      // Add the active class
+      li.classList.add(settings.nestedClass);
+
+      // Apply recursively to any parent navigation elements
+      activateNested(li, settings);
+    };
+
+    /**
+     * Activate a nav and content area
+     * @param  {Object} items    The nav item and content to activate
+     * @param  {Object} settings The settings for this instantiation
+     */
+    var activate = function (items, settings) {
+      // Make sure there are items to activate
+      if (!items) return;
+
+      // Get the parent list item
+      var li = items.nav.closest("li");
+      if (!li) return;
+
+      // Add the active class to the nav and content
+      li.classList.add(settings.navClass);
+      items.content.classList.add(settings.contentClass);
+
+      // Activate any parent navs in a nested navigation
+      activateNested(li, settings);
+
+      // Emit a custom event
+      emitEvent("gumshoeActivate", li, {
+        link: items.nav,
+        content: items.content,
+        settings: settings,
+      });
+    };
+
+    /**
+     * Create the Constructor object
+     * @param {String} selector The selector to use for navigation items
+     * @param {Object} options  User options and settings
+     */
+    var Constructor = function (selector, options) {
+      //
+      // Variables
+      //
+
+      var publicAPIs = {};
+      var navItems, contents, current, timeout, settings;
+
+      //
+      // Methods
+      //
+
+      /**
+       * Set variables from DOM elements
+       */
+      publicAPIs.setup = function () {
+        // Get all nav items
+        navItems = document.querySelectorAll(selector);
+
+        // Create contents array
+        contents = [];
+
+        // Loop through each item, get it's matching content, and push to the array
+        Array.prototype.forEach.call(navItems, function (item) {
+          // Get the content for the nav item
+          var content = document.getElementById(
+            decodeURIComponent(item.hash.substr(1)),
+          );
+          if (!content) return;
+
+          // Push to the contents array
+          contents.push({
+            nav: item,
+            content: content,
+          });
+        });
+
+        // Sort contents by the order they appear in the DOM
+        sortContents(contents);
+      };
+
+      /**
+       * Detect which content is currently active
+       */
+      publicAPIs.detect = function () {
+        // Get the active content
+        var active = getActive(contents, settings);
+
+        // if there's no active content, deactivate and bail
+        if (!active) {
+          if (current) {
+            deactivate(current, settings);
+            current = null;
+          }
+          return;
+        }
+
+        // If the active content is the one currently active, do nothing
+        if (current && active.content === current.content) return;
+
+        // Deactivate the current content and activate the new content
+        deactivate(current, settings);
+        activate(active, settings);
+
+        // Update the currently active content
+        current = active;
+      };
+
+      /**
+       * Detect the active content on scroll
+       * Debounced for performance
+       */
+      var scrollHandler = function (event) {
+        // If there's a timer, cancel it
+        if (timeout) {
+          window.cancelAnimationFrame(timeout);
+        }
+
+        // Setup debounce callback
+        timeout = window.requestAnimationFrame(publicAPIs.detect);
+      };
+
+      /**
+       * Update content sorting on resize
+       * Debounced for performance
+       */
+      var resizeHandler = function (event) {
+        // If there's a timer, cancel it
+        if (timeout) {
+          window.cancelAnimationFrame(timeout);
+        }
+
+        // Setup debounce callback
+        timeout = window.requestAnimationFrame(function () {
+          sortContents(contents);
+          publicAPIs.detect();
+        });
+      };
+
+      /**
+       * Destroy the current instantiation
+       */
+      publicAPIs.destroy = function () {
+        // Undo DOM changes
+        if (current) {
+          deactivate(current, settings);
+        }
+
+        // Remove event listeners
+        window.removeEventListener("scroll", scrollHandler, false);
+        if (settings.reflow) {
+          window.removeEventListener("resize", resizeHandler, false);
+        }
+
+        // Reset variables
+        contents = null;
+        navItems = null;
+        current = null;
+        timeout = null;
+        settings = null;
+      };
+
+      /**
+       * Initialize the current instantiation
+       */
+      var init = function () {
+        // Merge user options into defaults
+        settings = extend(defaults, options || {});
+
+        // Setup variables based on the current DOM
+        publicAPIs.setup();
+
+        // Find the currently active content
+        publicAPIs.detect();
+
+        // Setup event listeners
+        window.addEventListener("scroll", scrollHandler, false);
+        if (settings.reflow) {
+          window.addEventListener("resize", resizeHandler, false);
+        }
+      };
+
+      //
+      // Initialize and return the public APIs
+      //
+
+      init();
+      return publicAPIs;
+    };
+
+    //
+    // Return the Constructor
+    //
+
+    return Constructor;
+  },
+);
diff --git a/src/qiskit_sphinx_theme/assets/scripts/qiskit-sphinx-theme.js b/src/qiskit_sphinx_theme/assets/scripts/qiskit-sphinx-theme.js
index cf6e54c2..ff9bffa8 100644
--- a/src/qiskit_sphinx_theme/assets/scripts/qiskit-sphinx-theme.js
+++ b/src/qiskit_sphinx_theme/assets/scripts/qiskit-sphinx-theme.js
@@ -1,4 +1,181 @@
-// Empty file required by sphinx-theme-builder.
-//
-// This will allow us to fix Furo's JavaScript code to workaround
-// https://github.com/Qiskit/qiskit_sphinx_theme/issues/368.
+// This file is vendored from Furo's `assets/scripts/furo.js`. When adding custom Qiskit code,
+// surround it with `QISKIT CHANGE: start` and `QISKIT CHANGE: end` comments.
+
+import Gumshoe from "./gumshoe-patched.js";
+
+////////////////////////////////////////////////////////////////////////////////
+// Scroll Handling
+////////////////////////////////////////////////////////////////////////////////
+var tocScroll = null;
+var header = null;
+var lastScrollTop = window.pageYOffset || document.documentElement.scrollTop;
+const GO_TO_TOP_OFFSET = 64;
+
+function scrollHandlerForHeader() {
+  if (Math.floor(header.getBoundingClientRect().top) == 0) {
+    header.classList.add("scrolled");
+  } else {
+    header.classList.remove("scrolled");
+  }
+}
+
+function scrollHandlerForBackToTop(positionY) {
+  if (positionY < GO_TO_TOP_OFFSET) {
+    document.documentElement.classList.remove("show-back-to-top");
+  } else {
+    if (positionY < lastScrollTop) {
+      document.documentElement.classList.add("show-back-to-top");
+    } else if (positionY > lastScrollTop) {
+      document.documentElement.classList.remove("show-back-to-top");
+    }
+  }
+  lastScrollTop = positionY;
+}
+
+function scrollHandlerForTOC(positionY) {
+  if (tocScroll === null) {
+    return;
+  }
+
+  // top of page.
+  if (positionY == 0) {
+    tocScroll.scrollTo(0, 0);
+  } else if (
+    // bottom of page.
+    Math.ceil(positionY) >=
+    Math.floor(document.documentElement.scrollHeight - window.innerHeight)
+  ) {
+    tocScroll.scrollTo(0, tocScroll.scrollHeight);
+  } else {
+    // somewhere in the middle.
+    const current = document.querySelector(".scroll-current");
+    if (current == null) {
+      return;
+    }
+
+    // https://github.com/pypa/pip/issues/9159 This breaks scroll behaviours.
+    // // scroll the currently "active" heading in toc, into view.
+    // const rect = current.getBoundingClientRect();
+    // if (0 > rect.top) {
+    //   current.scrollIntoView(true); // the argument is "alignTop"
+    // } else if (rect.bottom > window.innerHeight) {
+    //   current.scrollIntoView(false);
+    // }
+  }
+}
+
+function scrollHandler(positionY) {
+  scrollHandlerForHeader();
+  scrollHandlerForBackToTop(positionY);
+  scrollHandlerForTOC(positionY);
+}
+
+////////////////////////////////////////////////////////////////////////////////
+// Theme Toggle
+////////////////////////////////////////////////////////////////////////////////
+function setTheme(mode) {
+  if (mode !== "light" && mode !== "dark" && mode !== "auto") {
+    console.error(`Got invalid theme mode: ${mode}. Resetting to auto.`);
+    mode = "auto";
+  }
+
+  document.body.dataset.theme = mode;
+  localStorage.setItem("theme", mode);
+  console.log(`Changed to ${mode} mode.`);
+}
+
+function cycleThemeOnce() {
+  const currentTheme = localStorage.getItem("theme") || "auto";
+  const prefersDark = window.matchMedia("(prefers-color-scheme: dark)").matches;
+
+  if (prefersDark) {
+    // Auto (dark) -> Light -> Dark
+    if (currentTheme === "auto") {
+      setTheme("light");
+    } else if (currentTheme == "light") {
+      setTheme("dark");
+    } else {
+      setTheme("auto");
+    }
+  } else {
+    // Auto (light) -> Dark -> Light
+    if (currentTheme === "auto") {
+      setTheme("dark");
+    } else if (currentTheme == "dark") {
+      setTheme("light");
+    } else {
+      setTheme("auto");
+    }
+  }
+}
+
+////////////////////////////////////////////////////////////////////////////////
+// Setup
+////////////////////////////////////////////////////////////////////////////////
+function setupScrollHandler() {
+  // Taken from https://developer.mozilla.org/en-US/docs/Web/API/Document/scroll_event
+  let last_known_scroll_position = 0;
+  let ticking = false;
+
+  window.addEventListener("scroll", function (e) {
+    last_known_scroll_position = window.scrollY;
+
+    if (!ticking) {
+      window.requestAnimationFrame(function () {
+        scrollHandler(last_known_scroll_position);
+        ticking = false;
+      });
+
+      ticking = true;
+    }
+  });
+  window.scroll();
+}
+
+function setupScrollSpy() {
+  if (tocScroll === null) {
+    return;
+  }
+
+  // Scrollspy -- highlight table on contents, based on scroll
+  new Gumshoe(".toc-tree a", {
+    reflow: true,
+    recursive: true,
+    navClass: "scroll-current",
+    offset: () => {
+      let rem = parseFloat(getComputedStyle(document.documentElement).fontSize);
+      // QISKIT CHANGE: start. Add 3.5rem for the Qiskit top nav bar.
+      // See _top-nav-bar.scss for where the value comes from.
+      return header.getBoundingClientRect().height + (0.5 * rem) + 1 + (3.5 * rem);
+      // QISKIT CHANGE: end.
+    },
+  });
+}
+
+function setupTheme() {
+  // Attach event handlers for toggling themes
+  const buttons = document.getElementsByClassName("theme-toggle");
+  Array.from(buttons).forEach((btn) => {
+    btn.addEventListener("click", cycleThemeOnce);
+  });
+}
+
+function setup() {
+  setupTheme();
+  setupScrollHandler();
+  setupScrollSpy();
+}
+
+////////////////////////////////////////////////////////////////////////////////
+// Main entrypoint
+////////////////////////////////////////////////////////////////////////////////
+function main() {
+  document.body.parentNode.classList.remove("no-js");
+
+  header = document.querySelector("header");
+  tocScroll = document.querySelector(".toc-scroll");
+
+  setup();
+}
+
+document.addEventListener("DOMContentLoaded", main);
diff --git a/src/qiskit_sphinx_theme/assets/styles/_top-nav-bar.scss b/src/qiskit_sphinx_theme/assets/styles/_top-nav-bar.scss
index ffb15674..e71096ee 100644
--- a/src/qiskit_sphinx_theme/assets/styles/_top-nav-bar.scss
+++ b/src/qiskit_sphinx_theme/assets/styles/_top-nav-bar.scss
@@ -1,5 +1,8 @@
 // This value is duplicated from `top-nav-bar.js`. Its definition of the variable is not
 // exposed globally. Keep in sync.
+//
+// Also keep in sync with `qiskit-sphinx-theme.js`, which adds the top nav bar
+// in the function `setupScrollSpy`.
 $top-nav-bar-height: 3.5rem;
 
 // Disable dark mode until qiskit.org has it: https://github.com/Qiskit/qiskit.org/issues/2310
@@ -58,10 +61,3 @@ div.header-left svg use {
     scroll-margin-top: calc(0.8rem + var(--header-height) + $top-nav-bar-height);
   }
 }
-
-// Turn off highlighting of the current page until we can properly solve
-// https://github.com/Qiskit/qiskit_sphinx_theme/issues/368.
-.toc-tree li.scroll-current > .reference {
-  color: var(--color-toc-item-text);
-  font-weight: unset;
-}
diff --git a/tests/js/snapshots.test.js-snapshots/right-side-bar-is-not-broken-by-our-page-layout-1-linux.png b/tests/js/snapshots.test.js-snapshots/right-side-bar-is-not-broken-by-our-page-layout-1-linux.png
index af7b2ff1..31fb8611 100644
Binary files a/tests/js/snapshots.test.js-snapshots/right-side-bar-is-not-broken-by-our-page-layout-1-linux.png and b/tests/js/snapshots.test.js-snapshots/right-side-bar-is-not-broken-by-our-page-layout-1-linux.png differ