diff --git a/pre_commit/commands/migrate_config.py b/pre_commit/commands/migrate_config.py
index 3f73bb83..47bb7695 100644
--- a/pre_commit/commands/migrate_config.py
+++ b/pre_commit/commands/migrate_config.py
@@ -21,8 +21,10 @@ def _migrate_map(contents):
     # Find the first non-header line
     lines = contents.splitlines(True)
     i = 0
-    while _is_header_line(lines[i]):
-        i += 1
+    # Only loop on non empty configuration file
+    if i < len(lines):
+        while _is_header_line(lines[i]):
+            i += 1
 
     header = ''.join(lines[:i])
     rest = ''.join(lines[i:])