diff --git a/api/internal/git/cloner.go b/api/internal/git/cloner.go
index d15fa75903..2098cdd31e 100644
--- a/api/internal/git/cloner.go
+++ b/api/internal/git/cloner.go
@@ -22,10 +22,16 @@ func ClonerUsingGitExec(repoSpec *RepoSpec) error {
 	if err = r.run("init"); err != nil {
 		return err
 	}
+	// git relative submodule need origin, see https://github.com/kubernetes-sigs/kustomize/issues/5131
+	if err = r.run("remote", "add", "origin", repoSpec.CloneSpec()); err != nil {
+		return err
+	}
 	ref := "HEAD"
 	if repoSpec.Ref != "" {
 		ref = repoSpec.Ref
 	}
+	// we use repoSpec.CloneSpec() instead of origin because on error,
+	// the prior prints the actual repo url for the user.
 	if err = r.run("fetch", "--depth=1", repoSpec.CloneSpec(), ref); err != nil {
 		return err
 	}
diff --git a/api/krusty/remoteloader_test.go b/api/krusty/remoteloader_test.go
index 58ffa30085..b38b578980 100644
--- a/api/krusty/remoteloader_test.go
+++ b/api/krusty/remoteloader_test.go
@@ -205,8 +205,8 @@ resources:
 resources:
 - file://$ROOT/with-submodule.git/submodule?ref=relative-submodule
 `,
-			// TODO(annasong): Replace with simpleBuild once #5131 is fixed.
-			err: `failed to run '\S+/git submodule update --init --recursive'`,
+
+			expected: simpleBuild,
 		},
 		{
 			name: "has timeout",