diff --git a/pre_commit/commands/migrate_config.py b/pre_commit/commands/migrate_config.py
index 3f73bb83..bac42319 100644
--- a/pre_commit/commands/migrate_config.py
+++ b/pre_commit/commands/migrate_config.py
@@ -21,7 +21,8 @@ def _migrate_map(contents):
     # Find the first non-header line
     lines = contents.splitlines(True)
     i = 0
-    while _is_header_line(lines[i]):
+    # Only loop on non empty configuration file
+    while i < len(lines) and _is_header_line(lines[i]):
         i += 1
 
     header = ''.join(lines[:i])
diff --git a/tests/commands/migrate_config_test.py b/tests/commands/migrate_config_test.py
index 8f9153fd..c58b9f74 100644
--- a/tests/commands/migrate_config_test.py
+++ b/tests/commands/migrate_config_test.py
@@ -147,3 +147,13 @@ def test_migrate_config_sha_to_rev(tmpdir):
         '    rev: v1.2.0\n'
         '    hooks: []\n'
     )
+
+
+@pytest.mark.parametrize('contents', ('', '\n'))
+def test_empty_configuration_file_user_error(tmpdir, contents):
+    cfg = tmpdir.join(C.CONFIG_FILE)
+    cfg.write(contents)
+    with tmpdir.as_cwd():
+        assert not migrate_config(C.CONFIG_FILE)
+    # even though the config is invalid, this should be a noop
+    assert cfg.read() == contents