diff --git a/scene/3d/skeleton_3d.cpp b/scene/3d/skeleton_3d.cpp
index 394a81c84b9..3e2b2b90583 100644
--- a/scene/3d/skeleton_3d.cpp
+++ b/scene/3d/skeleton_3d.cpp
@@ -543,6 +543,7 @@ bool Skeleton3D::is_show_rest_only() const {
 
 void Skeleton3D::clear_bones() {
 	bones.clear();
+	name_to_bone_index.clear();
 	process_order_dirty = true;
 	version++;
 	_make_dirty();