diff --git a/bootstrap.py b/bootstrap.py
index 7ed6823571fd8..db8feeedfd601 100755
--- a/bootstrap.py
+++ b/bootstrap.py
@@ -104,7 +104,8 @@ def run_cmd(cmd):
      'tools/maint/create_entry_points.py',
      'tools/pylauncher/pylauncher.exe',
      'tools/maint/run_python.bat',
-     'tools/maint/run_python.sh',
+     'tools/run_python.sh',
+     'tools/run_python_compiler.sh',
      'tools/maint/run_python.ps1',
    ], [sys.executable, 'tools/maint/create_entry_points.py']),
   ('git submodules', [
diff --git a/tools/maint/create_entry_points.py b/tools/maint/create_entry_points.py
index ead15389b2eda..ebc8b6ea52d35 100755
--- a/tools/maint/create_entry_points.py
+++ b/tools/maint/create_entry_points.py
@@ -6,10 +6,8 @@
 
 """Tool for creating/maintaining the python launcher scripts for emscripten tools.
 
-This tool makes copies or `run_python.sh/.bat` and `run_python_compiler.sh/.bat`
-script for each entry point. On UNIX we previously used symbolic links for
-simplicity but this breaks MINGW users on windows who want to use the shell script
-launcher but don't have symlink support.
+This tool creates symbolic links (on UNIX) or executables/batch scripts (on Windows)
+for each entry point.
 """
 
 import os
@@ -95,13 +93,13 @@ def main(all_platforms, use_bat_file):
   do_unix = all_platforms or not is_windows or is_msys2
   do_windows = all_platforms or is_windows
 
-  def generate_entry_points(cmd, path):
-    sh_file = path + '.sh'
-    bat_file = path + '.bat'
-    ps1_file = path + '.ps1'
-    sh_file = read_file(sh_file)
-    bat_file = read_file(bat_file)
-    ps1_file = read_file(ps1_file)
+  def generate_entry_points(cmd, name):
+    sh_file_path = os.path.join(__rootdir__, 'tools', name + '.sh')
+    bat_file_path = os.path.join(__scriptdir__, name + '.bat')
+    ps1_file_path = os.path.join(__scriptdir__, name + '.ps1')
+    sh_file = read_file(sh_file_path)
+    bat_file = read_file(bat_file_path)
+    ps1_file = read_file(ps1_file_path)
 
     for entry_point in cmd:
       sh_data = sh_file
@@ -114,8 +112,13 @@ def generate_entry_points(cmd, path):
 
       launcher = os.path.join(__rootdir__, entry_point)
       if do_unix:
-        write_file(launcher, sh_data)
-        make_executable(launcher)
+        if entry_point in entry_remap:
+          write_file(launcher, sh_data)
+          make_executable(launcher)
+        else:
+          target = os.path.relpath(sh_file_path, os.path.dirname(launcher))
+          maybe_remove(launcher)
+          os.symlink(target, launcher)
 
       if do_windows:
         maybe_remove(launcher + '.ps1')
@@ -126,8 +129,8 @@ def generate_entry_points(cmd, path):
         else:
           shutil.copyfile(windows_exe, launcher + '.exe')
 
-  generate_entry_points(entry_points, os.path.join(__scriptdir__, 'run_python'))
-  generate_entry_points(compiler_entry_points, os.path.join(__scriptdir__, 'run_python_compiler'))
+  generate_entry_points(entry_points, 'run_python')
+  generate_entry_points(compiler_entry_points, 'run_python_compiler')
 
 
 if __name__ == '__main__':
diff --git a/tools/maint/run_python.sh b/tools/run_python.sh
similarity index 80%
rename from tools/maint/run_python.sh
rename to tools/run_python.sh
index 7e507c13ba9c1..5b7c50af8e608 100755
--- a/tools/maint/run_python.sh
+++ b/tools/run_python.sh
@@ -5,11 +5,6 @@
 # found in the LICENSE file.
 #
 # Entry point for running python scripts on UNIX systems.
-#
-# Automatically generated by `create_entry_points.py`; DO NOT EDIT.
-#
-# To make modifications to this file, edit `tools/run_python.sh` and then run
-# `tools/maint/create_entry_points.py`
 
 # python -E does not ignore _PYTHON_SYSCONFIGDATA_NAME, an internal of cpython
 # used in cross compilation via setup.py, so we unset it explicitly here.
diff --git a/tools/maint/run_python_compiler.sh b/tools/run_python_compiler.sh
old mode 100644
new mode 100755
similarity index 80%
rename from tools/maint/run_python_compiler.sh
rename to tools/run_python_compiler.sh
index 32a246021a805..fe5cbecc1b25b
--- a/tools/maint/run_python_compiler.sh
+++ b/tools/run_python_compiler.sh
@@ -5,11 +5,6 @@
 # found in the LICENSE file.
 #
 # Entry point for running python scripts on UNIX systems.
-#
-# Automatically generated by `create_entry_points.py`; DO NOT EDIT.
-#
-# To make modifications to this file, edit `tools/maint/run_python_compiler.sh` and
-# then run `tools/maint/create_entry_points.py`
 
 # python -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
 # of cpython used in cross compilation via setup.py.