diff --git a/ChangeLog b/ChangeLog
index 1ad303a15..6d7911cd1 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -13,7 +13,9 @@ What's New in astroid 3.3.4?
 ============================
 Release date: TBA
 
+* Fix bug with ``manager.clear_cache()`` not fully clearing cache
 
+  Refs https://github.com/pylint-dev/pylint/pull/9932#issuecomment-2364985551
 
 What's New in astroid 3.3.3?
 ============================
diff --git a/astroid/manager.py b/astroid/manager.py
index e7c2c806f..e5398c45a 100644
--- a/astroid/manager.py
+++ b/astroid/manager.py
@@ -464,6 +464,8 @@ def clear_cache(self) -> None:
         _invalidate_cache()  # inference context cache
 
         self.astroid_cache.clear()
+        self._mod_file_cache.clear()
+
         # NB: not a new TransformVisitor()
         AstroidManager.brain["_transform"].transforms = collections.defaultdict(list)
 
diff --git a/tests/test_manager.py b/tests/test_manager.py
index 34ddd06d4..9a7bbdb7e 100644
--- a/tests/test_manager.py
+++ b/tests/test_manager.py
@@ -491,6 +491,32 @@ def test_clear_cache_clears_other_lru_caches(self) -> None:
                 # less equal because the "baseline" might have had multiple calls to bootstrap()
                 self.assertLessEqual(cleared_cache.currsize, baseline_cache.currsize)
 
+    def test_file_cache_after_clear_cache(self) -> None:
+        """Test to mimic the behavior of how pylint lints file and
+        ensure clear cache clears everything stored in the cache.
+        See https://github.com/pylint-dev/pylint/pull/9932#issuecomment-2364985551
+        for more information.
+        """
+        orig_sys_path = sys.path[:]
+        try:
+            search_path = resources.RESOURCE_PATH
+            sys.path.insert(0, search_path)
+            node = astroid.MANAGER.ast_from_file(resources.find("data/cache/a.py"))
+            self.assertEqual(node.name, "cache.a")
+
+            # This import from statement should succeed and update the astroid cache
+            importfrom_node = astroid.extract_node("from cache import a")
+            importfrom_node.do_import_module(importfrom_node.modname)
+        finally:
+            sys.path = orig_sys_path
+
+        astroid.MANAGER.clear_cache()
+
+        importfrom_node = astroid.extract_node("from cache import a")
+        # Try import from again after clear cache, this should raise an error
+        with self.assertRaises(AstroidBuildingError):
+            importfrom_node.do_import_module(importfrom_node.modname)
+
     def test_brain_plugins_reloaded_after_clearing_cache(self) -> None:
         astroid.MANAGER.clear_cache()
         format_call = astroid.extract_node("''.format()")
diff --git a/tests/testdata/python3/data/cache/__init__.py b/tests/testdata/python3/data/cache/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/testdata/python3/data/cache/a.py b/tests/testdata/python3/data/cache/a.py
new file mode 100644
index 000000000..9ddc377f3
--- /dev/null
+++ b/tests/testdata/python3/data/cache/a.py
@@ -0,0 +1 @@
+""" Test for clear cache. Doesn't need anything here"""