diff --git a/src/flake8/main/application.py b/src/flake8/main/application.py
index dc65f90..6c68305 100644
--- a/src/flake8/main/application.py
+++ b/src/flake8/main/application.py
@@ -131,8 +131,8 @@ class Application(object):
             pass
 
         opts, args = self.option_manager.parse_known_args(args)
-        # parse_known_args includes unknown options as args; get rid of them
-        args = [a for a in args if not a.startswith('-')]
+        # parse_known_args includes program name and unknown options as args
+        args = [a for a in args[1:] if not a.startswith('-')]
         self.prelim_opts, self.prelim_args = opts, args
 
     def exit(self):
diff --git a/tests/unit/test_application.py b/tests/unit/test_application.py
index abe940d..a281012 100644
--- a/tests/unit/test_application.py
+++ b/tests/unit/test_application.py
@@ -96,3 +96,13 @@ def test_returns_specified_plugin(application):
         assert execute is application.formatter_for('desired')
 
     assert warning.called is False
+
+
+def test_prelim_opts_args(application):
+    """Verify we get sensible prelim opts and args."""
+    application.parse_preliminary_options_and_args(
+        ['flake8', '--foo', '--verbose', 'src', 'setup.py', '--statistics'])
+
+    assert application.prelim_opts.statistics
+    assert application.prelim_opts.verbose
+    assert application.prelim_args == ['src', 'setup.py']