diff --git a/src/flake8/checker.py b/src/flake8/checker.py
index 7f148f4..ca9d835 100644
--- a/src/flake8/checker.py
+++ b/src/flake8/checker.py
@@ -247,8 +247,8 @@ class Manager(object):
                   '' if match else 'not ')
         return match
 
-    def make_checkers(self, paths=None):
-        # type: (List[str]) -> NoneType
+    def make_checkers(self, paths=None, is_cli=True):
+        # type: (List[str], bool) -> NoneType
         """Create checkers for each file."""
         if paths is None:
             paths = self.arguments
@@ -282,7 +282,11 @@ class Manager(object):
             # the event that the argument and the filename are identical.
             # If it was specified explicitly, the user intended for it to be
             # checked.
-            if argument == filename or should_create_file_checker(filename)
+            # EDIT(cold): Add ``is_cli`` to determine if the current process
+            # running in cli by using ``flake8 bin/script``. Otherwise
+            # it should be running by such as git hooks and etc.
+            if ((is_cli and argument == filename) or
+                should_create_file_checker(filename))
         ]
         LOG.info('Checking %d files', len(self.checkers))
 
@@ -360,15 +364,18 @@ class Manager(object):
         finally:
             self._force_cleanup()
 
-    def start(self, paths=None):
+    def start(self, paths=None, is_cli=True):
         """Start checking files.
 
         :param list paths:
             Path names to check. This is passed directly to
             :meth:`~Manager.make_checkers`.
+        :param bool is_cli:
+            If current process running in cli by using `flake8 script.py`
+            command.
         """
         LOG.info('Making checkers')
-        self.make_checkers(paths)
+        self.make_checkers(paths, is_cli)
         if not self.using_multiprocessing:
             return
 
diff --git a/src/flake8/main/application.py b/src/flake8/main/application.py
index 4765ee1..6fadb7e 100644
--- a/src/flake8/main/application.py
+++ b/src/flake8/main/application.py
@@ -227,7 +227,7 @@ class Application(object):
                 checker_plugins=self.check_plugins,
             )
 
-    def run_checks(self, files=None):
+    def run_checks(self, files=None, is_cli=True):
         # type: (Union[List[str], NoneType]) -> NoneType
         """Run the actual checks with the FileChecker Manager.
 
@@ -237,10 +237,14 @@ class Application(object):
 
         :param list files:
             List of filenames to process
+
+        :param bool is_cli:
+            If current process running in cli by using `flake8 script.py`
+            command.
         """
         if self.running_against_diff:
             files = list(sorted(self.parsed_diff.keys()))
-        self.file_checker_manager.start(files)
+        self.file_checker_manager.start(files, is_cli=is_cli)
         self.file_checker_manager.run()
         LOG.info('Finished running')
         self.file_checker_manager.stop()
diff --git a/src/flake8/main/git.py b/src/flake8/main/git.py
index 5ff0fc7..b5bee01 100644
--- a/src/flake8/main/git.py
+++ b/src/flake8/main/git.py
@@ -5,7 +5,6 @@
 
 """
 import contextlib
-import fnmatch
 import os
 import shutil
 import stat
@@ -41,11 +40,10 @@ def hook(lazy=False, strict=False):
     from flake8.main import application
     app = application.Application()
     with make_temporary_directory() as tempdir:
-        filepaths = [x for x in list(copy_indexed_files_to(tempdir, lazy))
-                     if fnmatch.fnmatch(x, '*.py')]
+        filepaths = list(copy_indexed_files_to(tempdir, lazy))
         app.initialize(['.'])
         app.options.exclude = update_excludes(app.options.exclude, tempdir)
-        app.run_checks(filepaths)
+        app.run_checks(filepaths, is_cli=False)
 
     app.report_errors()
     if strict:
diff --git a/tests/unit/test_git.py b/tests/unit/test_git.py
index 0a063b0..a798188 100644
--- a/tests/unit/test_git.py
+++ b/tests/unit/test_git.py
@@ -30,17 +30,29 @@ def test_find_modified_files(lazy):
 
 
 @mock.patch("flake8.main.git.copy_indexed_files_to")
-def test_only_py_files(mock_files):
+@mock.patch("flake8.checker.os.path.exists", autospec=True)
+@mock.patch("flake8.checker.FileChecker._make_processor", autospec=True)
+def test_only_py_files(mock_processor, mock_exists, mock_files):
     """Confirm only run checks on Python source file."""
+    class MockProcessor(object):
+        def __init__(self, filename):
+            self.filename = filename
+            self.lines = []
+
+    mock_processor.side_effect = lambda self: MockProcessor(self.filename)
+    mock_exists.return_value = True
     mock_files.return_value = [
         "/tmp/xxx/test.py",
         "/tmp/xxx/test.html",
         "/tmp/xxx/test.txt",
     ]
 
-    spec = "flake8.main.application.Application.run_checks"
-    with mock.patch(spec) as mock_run:
+    def _run_to_test_checker(self):
+        new_paths = [x.filename for x in self.checkers]
+        assert "/tmp/xxx/test.py" in new_paths
+        assert "/tmp/xxx/test.html" not in new_paths
+        assert "/tmp/xxx/test.txt" not in new_paths
+
+    with mock.patch("flake8.checker.Manager.run", autospec=True) as mock_run:
+        mock_run.side_effect = _run_to_test_checker
         git.hook(lazy=False)
-        mock_run.assert_called_once_with([
-            "/tmp/xxx/test.py"
-        ])