diff --git a/scripts/firecloud_api/firecloud_api.py b/scripts/firecloud_api/firecloud_api.py
index 884728d333..4ba1456a33 100644
--- a/scripts/firecloud_api/firecloud_api.py
+++ b/scripts/firecloud_api/firecloud_api.py
@@ -172,6 +172,9 @@ def upload_test_inputs(self, pipeline_name, test_inputs, branch_name):
         # update the config with the new branch name
         print(f"Updating methodVersion with branch name: {branch_name}")
         config["methodRepoMethod"]["methodVersion"] = branch_name
+
+        # Increment the methodConfigVersion
+        config["methodConfigVersion"] += 1  # Increment version number by  1
         print(f"Updated method configuration: {config}")