diff --git a/pre_commit/clientlib.py b/pre_commit/clientlib.py
index 962c7fa8f..bc7274a7d 100644
--- a/pre_commit/clientlib.py
+++ b/pre_commit/clientlib.py
@@ -216,14 +216,14 @@ def warn_unknown_keys_repo(
     (
         'check-hooks-apply', (
             ('name', 'Check hooks apply to the repository'),
-            ('files', C.CONFIG_FILE),
+            ('files', f'^{re.escape(C.CONFIG_FILE)}$'),
             ('entry', _entry('check_hooks_apply')),
         ),
     ),
     (
         'check-useless-excludes', (
             ('name', 'Check for useless excludes'),
-            ('files', C.CONFIG_FILE),
+            ('files', f'^{re.escape(C.CONFIG_FILE)}$'),
             ('entry', _entry('check_useless_excludes')),
         ),
     ),
diff --git a/tests/clientlib_test.py b/tests/clientlib_test.py
index 09bdb3ee9..da794e6e7 100644
--- a/tests/clientlib_test.py
+++ b/tests/clientlib_test.py
@@ -1,4 +1,5 @@
 import logging
+import re
 
 import cfgv
 import pytest
@@ -10,6 +11,7 @@
 from pre_commit.clientlib import CONFIG_SCHEMA
 from pre_commit.clientlib import DEFAULT_LANGUAGE_VERSION
 from pre_commit.clientlib import MANIFEST_SCHEMA
+from pre_commit.clientlib import META_HOOK_DICT
 from pre_commit.clientlib import MigrateShaToRev
 from pre_commit.clientlib import validate_config_main
 from pre_commit.clientlib import validate_manifest_main
@@ -392,6 +394,15 @@ def test_meta_hook_invalid(config_repo):
         cfgv.validate(config_repo, CONFIG_REPO_DICT)
 
 
+def test_meta_check_hooks_apply_only_at_top_level():
+    cfg = {'id': 'check-hooks-apply'}
+    cfg = cfgv.apply_defaults(cfg, META_HOOK_DICT)
+
+    files_re = re.compile(cfg['files'])
+    assert files_re.search('.pre-commit-config.yaml')
+    assert not files_re.search('foo/.pre-commit-config.yaml')
+
+
 @pytest.mark.parametrize(
     'mapping',
     (