diff --git a/mercurial/patch.py b/mercurial/patch.py
--- a/mercurial/patch.py
+++ b/mercurial/patch.py
@@ -20,6 +20,7 @@
 from .i18n import _
 from .node import (
     hex,
+    nullhex,
     short,
 )
 from .pycompat import open
@@ -3099,11 +3100,13 @@
 
     ctx1, fctx1, path1, flag1, content1, date1 = data1
     ctx2, fctx2, path2, flag2, content2, date2 = data2
+    index1 = _gitindex(content1) if path1 in ctx1 else nullhex
+    index2 = _gitindex(content2) if path2 in ctx2 else nullhex
     if binary and opts.git and not opts.nobinary:
         text = mdiff.b85diff(content1, content2)
         if text:
             header.append(
-                b'index %s..%s' % (_gitindex(content1), _gitindex(content2))
+                b'index %s..%s' % (index1, index2)
             )
         hunks = ((None, [text]),)
     else:
@@ -3114,8 +3117,8 @@
             header.append(
                 b'index %s..%s %s'
                 % (
-                    _gitindex(content1)[0 : opts.index],
-                    _gitindex(content2)[0 : opts.index],
+                    index1[0 : opts.index],
+                    index2[0 : opts.index],
                     _gitmode[flag],
                 )
             )
diff --git a/tests/test-diff-unified.t b/tests/test-diff-unified.t
--- a/tests/test-diff-unified.t
+++ b/tests/test-diff-unified.t
@@ -467,7 +467,7 @@
   $ hg ci -Am "empty a"
   adding a
   $ hg diff -c 0 --git --config experimental.extendedheader.index=full | grep index
-  index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
+  index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
 
 Make sure `hg diff --git` differentiate "file was empty" and "file is removed"
 for git blob oids
@@ -476,6 +476,6 @@
   $ hg ci -Am "removed a"
   removing a
   $ hg diff -c 1 --git --config experimental.extendedheader.index=full | grep index
-  index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
+  index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 100644
 
   $ cd ..