diff --git a/tools/workspace/pybind11/package.BUILD.bazel b/tools/workspace/pybind11/package.BUILD.bazel
index 1682beaff295..37b34304657f 100644
--- a/tools/workspace/pybind11/package.BUILD.bazel
+++ b/tools/workspace/pybind11/package.BUILD.bazel
@@ -5,43 +5,56 @@ load(
     "install",
     "install_files",
 )
+load(
+    "@drake//tools/workspace:check_lists_consistency.bzl",
+    "check_lists_consistency",
+)
 load("@drake//tools/lint:python_lint.bzl", "python_lint")
 
 licenses(["notice"])  # BSD-3-Clause
 
 package(default_visibility = ["//visibility:public"])
 
+_HDRS = [
+    "include/pybind11/attr.h",
+    "include/pybind11/buffer_info.h",
+    "include/pybind11/cast.h",
+    "include/pybind11/chrono.h",
+    "include/pybind11/common.h",
+    "include/pybind11/complex.h",
+    "include/pybind11/detail/class.h",
+    "include/pybind11/detail/common.h",
+    "include/pybind11/detail/descr.h",
+    "include/pybind11/detail/init.h",
+    "include/pybind11/detail/internals.h",
+    "include/pybind11/detail/type_caster_base.h",
+    "include/pybind11/detail/typeid.h",
+    "include/pybind11/eigen.h",
+    "include/pybind11/embed.h",
+    "include/pybind11/eval.h",
+    "include/pybind11/functional.h",
+    "include/pybind11/gil.h",
+    "include/pybind11/iostream.h",
+    "include/pybind11/numpy.h",
+    "include/pybind11/operators.h",
+    "include/pybind11/options.h",
+    "include/pybind11/pybind11.h",
+    "include/pybind11/pytypes.h",
+    "include/pybind11/stl.h",
+    "include/pybind11/stl/filesystem.h",
+    "include/pybind11/stl_bind.h",
+]
+
+check_lists_consistency(
+    files = _HDRS,
+    glob_include = [
+        "include/**",
+    ],
+)
+
 cc_library(
     name = "pybind11",
-    hdrs = [
-        "include/pybind11/attr.h",
-        "include/pybind11/buffer_info.h",
-        "include/pybind11/cast.h",
-        "include/pybind11/chrono.h",
-        "include/pybind11/common.h",
-        "include/pybind11/complex.h",
-        "include/pybind11/detail/class.h",
-        "include/pybind11/detail/common.h",
-        "include/pybind11/detail/descr.h",
-        "include/pybind11/detail/init.h",
-        "include/pybind11/detail/internals.h",
-        "include/pybind11/detail/type_caster_base.h",
-        "include/pybind11/detail/typeid.h",
-        "include/pybind11/eigen.h",
-        "include/pybind11/embed.h",
-        "include/pybind11/eval.h",
-        "include/pybind11/functional.h",
-        "include/pybind11/gil.h",
-        "include/pybind11/iostream.h",
-        "include/pybind11/numpy.h",
-        "include/pybind11/operators.h",
-        "include/pybind11/options.h",
-        "include/pybind11/pybind11.h",
-        "include/pybind11/pytypes.h",
-        "include/pybind11/stl.h",
-        "include/pybind11/stl/filesystem.h",
-        "include/pybind11/stl_bind.h",
-    ],
+    hdrs = _HDRS,
     includes = ["include"],
     deps = [
         "@eigen",