diff --git a/flask_annex/file.py b/flask_annex/file.py
index 45e1944..6ed8cf0 100644
--- a/flask_annex/file.py
+++ b/flask_annex/file.py
@@ -19,7 +19,13 @@ def _get_filename(self, key):
         return flask.safe_join(self._root_path, key)
 
     def delete(self, key):
-        os.unlink(self._get_filename(key))
+        try:
+            os.unlink(self._get_filename(key))
+        except OSError as e:
+            if e.errno != errno.ENOENT:
+                # It's fine if the file doesn't exist.
+                raise  # pragma: no cover
+
         self._clean_empty_dirs(key)
 
     def _clean_empty_dirs(self, key):
@@ -30,9 +36,10 @@ def _clean_empty_dirs(self, key):
             try:
                 os.rmdir(dir_name)
             except OSError as e:
-                if e.errno != errno.ENOTEMPTY:
+                if e.errno == errno.ENOTEMPTY:
+                    break
+                if e.errno != errno.ENOENT:
                     raise  # pragma: no cover
-                break
 
             key_dir_name = os.path.dirname(key_dir_name)
 
diff --git a/tests/helpers.py b/tests/helpers.py
index c583507..9c90042 100644
--- a/tests/helpers.py
+++ b/tests/helpers.py
@@ -74,7 +74,10 @@ def test_delete(self, annex):
         annex.delete('foo/bar.txt')
         assert not annex.list_keys('foo/bar.txt')
 
+    def test_delete_nonexistent(self, annex):
+        annex.delete('@@nonexistent')
+
     def test_delete_many(self, annex):
         assert annex.list_keys('')
-        annex.delete_many(('foo/bar.txt', 'foo/baz.json'))
+        annex.delete_many(('foo/bar.txt', 'foo/baz.json', 'foo/@@nonexistent'))
         assert not annex.list_keys('')