diff --git a/CHANGES.rst b/CHANGES.rst
index 8f9559e85d7..fe6ebc871ca 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -4,6 +4,9 @@ Release 7.3.3 (in development)
 Bugs fixed
 ----------
 
+* #12290: Fix a false-positive warning when setting a configuration value
+  with ``Any`` as the valid type to a type other than the value's default.
+  Patch by Adam Turner.
 
 Release 7.3.2 (released Apr 17, 2024)
 =====================================
diff --git a/sphinx/config.py b/sphinx/config.py
index 29148a53afe..84e20f6e59f 100644
--- a/sphinx/config.py
+++ b/sphinx/config.py
@@ -658,7 +658,7 @@ def check_confval_types(app: Sphinx | None, config: Config) -> None:
         if default is None and not valid_types:
             continue  # neither inferable nor explicitly annotated types
 
-        if valid_types is Any:  # any type of value is accepted
+        if valid_types == frozenset({Any}):  # any type of value is accepted
             continue
 
         if isinstance(valid_types, ENUM):
diff --git a/tests/test_config/test_config.py b/tests/test_config/test_config.py
index d269b7169b0..ea9eadb2397 100644
--- a/tests/test_config/test_config.py
+++ b/tests/test_config/test_config.py
@@ -5,7 +5,7 @@
 import time
 from collections import Counter
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 from unittest import mock
 
 import pytest
@@ -552,6 +552,14 @@ def test_check_enum_for_list_failed(logger):
     assert logger.warning.called
 
 
+@mock.patch("sphinx.config.logger")
+def test_check_any(logger):
+    config = Config({'value': None})
+    config.add('value', 'default', '', Any)
+    check_confval_types(None, config)
+    logger.warning.assert_not_called()  # not warned
+
+
 nitpick_warnings = [
     "WARNING: py:const reference target not found: prefix.anything.postfix",
     "WARNING: py:class reference target not found: prefix.anything",