diff --git a/builtin/checkout.c b/builtin/checkout.c
index 91f8509f85..27daa09c3c 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -126,6 +126,7 @@ static int update_some(const struct object_id *oid, struct strbuf *base,
 	if (pos >= 0) {
 		struct cache_entry *old = active_cache[pos];
 		if (ce->ce_mode == old->ce_mode &&
+		    !ce_intent_to_add(old) &&
 		    oideq(&ce->oid, &old->oid)) {
 			old->ce_flags |= CE_UPDATE;
 			discard_cache_entry(ce);
diff --git a/t/t2022-checkout-paths.sh b/t/t2022-checkout-paths.sh
index fc3eb43b89..6844afafc0 100755
--- a/t/t2022-checkout-paths.sh
+++ b/t/t2022-checkout-paths.sh
@@ -78,4 +78,15 @@ test_expect_success 'do not touch files that are already up-to-date' '
 	test_cmp expect actual
 '
 
+test_expect_success 'checkout HEAD adds deleted intent-to-add file back to index' '
+	echo "nonempty" >nonempty &&
+	>empty &&
+	git add nonempty empty &&
+	git commit -m "create files to be deleted" &&
+	git rm --cached nonempty empty &&
+	git add -N nonempty empty &&
+	git checkout HEAD nonempty empty &&
+	git diff --cached --exit-code
+'
+
 test_done