diff --git a/autoload/tagbar.vim b/autoload/tagbar.vim
index 35ceae2c..b73fb7b9 100644
--- a/autoload/tagbar.vim
+++ b/autoload/tagbar.vim
@@ -3093,7 +3093,7 @@ endfunction
 
 " run shell command in a proper way: prevent temporary window creation
 function! s:run_system(cmd, version) abort
-    if has('win32') && !has('nvim') && a:version > 0 && (has('python3') || has('python2'))
+    if has('win32') && !has('nvim') && && !has('gui_running') && a:version > 0 && (has('python3') || has('python2'))
         if a:version == 3 && has('python3')
             let pyx = 'py3 '
             let python_eval = 'py3eval'