diff --git a/scripts/jobrunner.py b/scripts/jobrunner.py
index f171c81..552e4ff 100755
--- a/scripts/jobrunner.py
+++ b/scripts/jobrunner.py
@@ -143,9 +143,11 @@ def main():
         os.makedirs(config["workdir"])
         jr_logger.info(f"Creating work directory at {config['workdir']}")
 
-    config["catalog-service-url"] = ee2_url.replace("ee2", "catalog")
+    #Expect the url to be something like kbase.us/services/ee2 or /services/ee2-nr
+    ee2_suffix = ee2_url.split("/")[-1]
+    config["catalog-service-url"] = ee2_url.replace(ee2_suffix, "catalog")
     auth_ext = "auth/api/legacy/KBase/Sessions/Login"
-    config["auth-service-url"] = ee2_url.replace("ee2", auth_ext)
+    config["auth-service-url"] = ee2_url.replace(ee2_suffix, f"{auth_ext}")
 
     # WARNING: Condor job environment may not inherit from system ENV
     if "USE_SHIFTER" in os.environ: