diff --git a/pre_commit/meta_hooks/check_hooks_apply.py b/pre_commit/meta_hooks/check_hooks_apply.py
index 8c9a92d8..20d7f069 100644
--- a/pre_commit/meta_hooks/check_hooks_apply.py
+++ b/pre_commit/meta_hooks/check_hooks_apply.py
@@ -14,6 +14,8 @@ def check_all_hooks_match_files(config_file):
 
     for repo in runner.repositories:
         for hook_id, hook in repo.hooks:
+            if hook['always_run']:
+                continue
             include, exclude = hook['files'], hook['exclude']
             filtered = _filter_by_include_exclude(files, include, exclude)
             types, exclude_types = hook['types'], hook['exclude_types']
diff --git a/tests/meta_hooks/check_hooks_apply_test.py b/tests/meta_hooks/check_hooks_apply_test.py
index 0ca68802..86bc598d 100644
--- a/tests/meta_hooks/check_hooks_apply_test.py
+++ b/tests/meta_hooks/check_hooks_apply_test.py
@@ -116,6 +116,12 @@ def test_valid_includes(
                 OrderedDict((
                     ('id', 'check-useless-excludes'),
                 )),
+                # Should not be reported as an error due to always_run
+                OrderedDict((
+                    ('id', 'check-useless-excludes'),
+                    ('files', '^$'),
+                    ('always_run', True),
+                )),
             ),
         ),
     ))