diff --git a/.circleci/config.yml b/.circleci/config.yml
index a15021754d835..474c00e156779 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -57,7 +57,7 @@ commands:
   bootstrap:
     description: "bootstrap"
     steps:
-      - run: ./bootstrap
+      - run: "$EMSDK_PYTHON ./bootstrap.py"
   pip-install:
     description: "pip install"
     parameters:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index be9dfcd59af6f..c3a1cf2d56c7f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -60,7 +60,7 @@ jobs:
           # Uncomment this like to pull the rebaseline_tests.py from the
           # current branch:
           # git checkout - ./tools/maint/rebaseline_tests.py
-          ./bootstrap
+          ./bootstrap.py
           if ! ./tools/maint/rebaseline_tests.py --check-only; then
             echo ""
             echo "Test expectations are out-of-date on the target branch."
@@ -83,7 +83,7 @@ jobs:
           # since it doesn't recognise it.
           git checkout ${{ github.sha }}
           git rev-parse HEAD
-          ./bootstrap
+          ./bootstrap.py
           if ! ./tools/maint/rebaseline_tests.py --check-only --clear-cache; then
             echo "Test expectations are out-of-date on the PR branch."
             echo "You can run './tools/maint/rebaseline_tests.py' to"
diff --git a/.gitignore b/.gitignore
index f2394642782cb..234517cc97797 100644
--- a/.gitignore
+++ b/.gitignore
@@ -91,7 +91,6 @@ test/runner.bat
 tools/file_packager.bat
 tools/webidl_binder.bat
 
-bootstrap.exe
 em++.exe
 emcc.exe
 em-config.exe
diff --git a/bootstrap b/bootstrap
deleted file mode 100755
index 7e507c13ba9c1..0000000000000
--- a/bootstrap
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh
-# Copyright 2020 The Emscripten Authors.  All rights reserved.
-# Emscripten is available under two separate licenses, the MIT license and the
-# University of Illinois/NCSA Open Source License.  Both these licenses can be
-# 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.
-unset _PYTHON_SYSCONFIGDATA_NAME
-
-_EM_PY=$EMSDK_PYTHON
-
-if [ -z "$_EM_PY" ]; then
-  _EM_PY=$(command -v python3 2> /dev/null)
-fi
-
-if [ -z "$_EM_PY" ]; then
-  _EM_PY=$(command -v python 2> /dev/null)
-fi
-
-if [ -z "$_EM_PY" ]; then
-  echo 'unable to find python in $PATH'
-  exit 1
-fi
-
-exec "$_EM_PY" -E "$0.py" "$@"
diff --git a/bootstrap.bat b/bootstrap.bat
deleted file mode 100644
index e9080623b77f0..0000000000000
--- a/bootstrap.bat
+++ /dev/null
@@ -1,86 +0,0 @@
-:: Entry point for running python scripts on windows systems.
-::
-:: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
-::
-:: To make modifications to this file, edit `tools\run_python.bat` and then run
-:: `tools\maint\create_entry_points.py`
-
-:: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
-:: or there will be a parsing error.
-
-:: All env. vars specified in this file are to be local only to this script.
-@setlocal
-:: -E will not ignore _PYTHON_SYSCONFIGDATA_NAME an internal
-:: of cpython used in cross compilation via setup.py.
-@set _PYTHON_SYSCONFIGDATA_NAME=
-@set _EM_PY=%EMSDK_PYTHON%
-@if "%_EM_PY%"=="" (
-  set _EM_PY=python
-)
-
-:: Work around Windows bug https://github.com/microsoft/terminal/issues/15212 : If this
-:: script is invoked via enclosing the invocation in quotes via PATH lookup, then %~f0 and
-:: %~dp0 expansions will not work.
-:: So first try if %~dp0 might work, and if not, manually look up this script from PATH.
-@if exist "%~f0" (
-  set "MYDIR=%~dp0"
-  goto FOUND_MYDIR
-)
-@for %%I in (%~n0.bat) do (
-  @if exist %%~$PATH:I (
-    set MYDIR=%%~dp$PATH:I
-  ) else (
-    echo Fatal Error! Due to a Windows bug, we are unable to locate the path to %~n0.bat.
-    echo To help this issue, try removing unnecessary quotes in the invocation of emcc,
-    echo or add Emscripten directory to PATH.
-    echo See github.com/microsoft/terminal/issues/15212 and
-    echo github.com/emscripten-core/emscripten/issues/19207 for more details.
-  )
-)
-:FOUND_MYDIR
-
-:: Python Windows bug https://bugs.python.org/issue34780: If this script was invoked via a
-:: shared stdin handle from the parent process, and that parent process stdin handle is in
-:: a certain state, running python.exe might hang here. To work around this, if
-:: EM_WORKAROUND_PYTHON_BUG_34780 is defined, invoke python with '< NUL' stdin to avoid
-:: sharing the parent's stdin handle to it, avoiding the hang.
-
-:: On Windows 7, the compiler batch scripts are observed to exit with a non-zero errorlevel,
-:: even when the python executable above did succeed and quit with errorlevel 0 above.
-:: On Windows 8 and newer, this issue has not been observed. It is possible that this
-:: issue is related to the above python bug, but this has not been conclusively confirmed,
-:: so using a separate env. var EM_WORKAROUND_WIN7_BAD_ERRORLEVEL_BUG to enable the known
-:: workaround this issue, which is to explicitly quit the calling process with the previous
-:: errorlevel from the above command.
-
-:: Also must use goto to jump to the command dispatch, since we cannot invoke emcc from
-:: inside a if() block, because if a cmdline param would contain a char '(' or ')', that
-:: would throw off the parsing of the cmdline arg.
-@if "%EM_WORKAROUND_PYTHON_BUG_34780%"=="" (
-  @if "%EM_WORKAROUND_WIN7_BAD_ERRORLEVEL_BUG%"=="" (
-    goto NORMAL
-  ) else (
-    goto NORMAL_EXIT
-  )
-) else (
-  @if "%EM_WORKAROUND_WIN7_BAD_ERRORLEVEL_BUG%"=="" (
-    goto MUTE_STDIN
-  ) else (
-    goto MUTE_STDIN_EXIT
-  )
-)
-
-:NORMAL_EXIT
-@"%_EM_PY%" -E "%MYDIR%%~n0.py" %*
-@exit %ERRORLEVEL%
-
-:MUTE_STDIN
-@"%_EM_PY%" -E "%MYDIR%%~n0.py" %* < NUL
-@exit /b %ERRORLEVEL%
-
-:MUTE_STDIN_EXIT
-@"%_EM_PY%" -E "%MYDIR%%~n0.py" %* < NUL
-@exit %ERRORLEVEL%
-
-:NORMAL
-@"%_EM_PY%" -E "%MYDIR%%~n0.py" %*
diff --git a/bootstrap.py b/bootstrap.py
index 777fee3fa99df..00375cac33724 100755
--- a/bootstrap.py
+++ b/bootstrap.py
@@ -61,7 +61,7 @@ def check_deps(name, deps):
 def check():
   for name, deps, _ in actions:
     if not check_deps(name, deps):
-      utils.exit_with_error(f'emscripten setup is not complete ("{name}" is out-of-date). Run `bootstrap` to update')
+      utils.exit_with_error(f'emscripten setup is not complete ("{name}" is out-of-date). Run `bootstrap.py` to update')
 
 
 def main(args):
diff --git a/tools/maint/create_entry_points.py b/tools/maint/create_entry_points.py
index 0cc033132c2c3..8f210706c2a68 100755
--- a/tools/maint/create_entry_points.py
+++ b/tools/maint/create_entry_points.py
@@ -26,7 +26,6 @@
 '''.split()
 
 entry_points = '''
-bootstrap
 emar
 embuilder
 emcmake
@@ -115,10 +114,6 @@ def generate_entry_points(cmd, path):
         make_executable(launcher)
 
       if do_windows:
-        if entry_point != 'bootstrap':
-          # The bootstrap.bat file is checked into source control so we
-          # don't want to delete it.
-          maybe_remove(launcher + '.bat')
         maybe_remove(launcher + '.ps1')
         maybe_remove(launcher + '.exe')
         if use_bat_file:
diff --git a/tools/maint/post-checkout b/tools/maint/post-checkout
index c4838f1ac1940..f18b7dd6b01d2 100755
--- a/tools/maint/post-checkout
+++ b/tools/maint/post-checkout
@@ -10,4 +10,4 @@
 
 # Test for the existence of the bootstrap script itself to handle branches
 # that predate its existence.
-test -f ./bootstrap && exec ./bootstrap
+test -f ./bootstrap.py && exec ./bootstrap.py