diff --git a/emsdk.py b/emsdk.py
index 8ae6b0703b..a2a6bc5ba0 100644
--- a/emsdk.py
+++ b/emsdk.py
@@ -129,7 +129,7 @@ def exit_with_error(msg):
   else:
     BASH = True
 
-if WINDOWS:
+if WINDOWS and not MSYS:
   ENVPATH_SEPARATOR = ';'
 else:
   ENVPATH_SEPARATOR = ':'