diff --git a/cwltool/main.py b/cwltool/main.py
index 63e3d86793..ba6666f469 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -1011,7 +1011,9 @@ def main(
                 argsl = sys.argv[1:]
             addl = []  # type: List[str]
             if "CWLTOOL_OPTIONS" in os.environ:
-                addl = os.environ["CWLTOOL_OPTIONS"].split(" ")
+                c_opts = os.environ["CWLTOOL_OPTIONS"].split(" ")
+                if len(c_opts) > 1 or c_opts[0] != "":
+                    addl = c_opts
             parser = arg_parser()
             argcomplete.autocomplete(parser)
             args = parser.parse_args(addl + argsl)