diff --git a/Makefile.envs b/Makefile.envs
index a204910c4..ae202adcd 100644
--- a/Makefile.envs
+++ b/Makefile.envs
@@ -1,7 +1,7 @@
 export PYVERSION ?= 3.10.2
 # Note: when updating EMSCRIPTEN_VERSION make sure to update
 # the version number in the "uname" patch.
-export PYODIDE_EMSCRIPTEN_VERSION ?= 3.1.20
+export PYODIDE_EMSCRIPTEN_VERSION ?= 3.1.21
 
 export PLATFORM_TRIPLET=wasm32-emscripten
 export SYSCONFIG_NAME=_sysconfigdata__emscripten_$(PLATFORM_TRIPLET)
diff --git a/docs/project/changelog.md b/docs/project/changelog.md
index 24852cf3f..6290ed1cd 100644
--- a/docs/project/changelog.md
+++ b/docs/project/changelog.md
@@ -14,8 +14,8 @@ substitutions:
 
 ## Unreleased
 
-- {{ Enhancement }} Emscripten was updated to Version 3.1.20
-  {pr}`2958`, {pr}`2950`, {pr}`3027`
+- {{ Enhancement }} Emscripten was updated to Version 3.1.21
+  {pr}`2958`, {pr}`2950`, {pr}`3027`, {pr}`3107`
 
 - {{ Enhancement }} Implemented `reverse`, `__reversed__`, `count`, `index`,
   `append`, and `pop` for `JsProxy` of Javascript arrays.
diff --git a/emsdk/patches/0001-Fix-assertion-in-file_packager-for-Jest.patch b/emsdk/patches/0001-Fix-assertion-in-file_packager-for-Jest.patch
deleted file mode 100644
index 7acd19613..000000000
--- a/emsdk/patches/0001-Fix-assertion-in-file_packager-for-Jest.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From 86ae308adb000ee1243aa8d7b106cdd49a18153e Mon Sep 17 00:00:00 2001
-From: Hood Chatham <roberthoodchatham@gmail.com>
-Date: Wed, 24 Aug 2022 16:24:48 -0700
-Subject: [PATCH] Fix assertion in file_packager for Jest
-
----
- tools/file_packager.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tools/file_packager.py b/tools/file_packager.py
-index 7d48556d6..d608f6738 100755
---- a/tools/file_packager.py
-+++ b/tools/file_packager.py
-@@ -996,7 +996,7 @@ def generate_js(data_target, data_files, metadata):
-     code += '''
-       function processPackageData(arrayBuffer) {
-         assert(arrayBuffer, 'Loading data file failed.');
--        assert(arrayBuffer instanceof ArrayBuffer, 'bad input to processPackageData');
-+        assert(arrayBuffer.constructor.name === ArrayBuffer.name, 'bad input to processPackageData');
-         var byteArray = new Uint8Array(arrayBuffer);
-         var curr;
-         %s
--- 
-2.25.1
-
diff --git a/src/tests/test_cmdline_runner.py b/src/tests/test_cmdline_runner.py
index 52a416910..53ff8b942 100644
--- a/src/tests/test_cmdline_runner.py
+++ b/src/tests/test_cmdline_runner.py
@@ -233,7 +233,7 @@ def clean_pkg_install_stdout(stdout: str) -> str:
     stdout = re.sub(r"^  .*?\n", "", stdout, flags=re.MULTILINE)
     stdout = re.sub(r"^\[notice\].*?\n", "", stdout, flags=re.MULTILINE)
     # Remove version numbers
-    stdout = re.sub(r"(?<=[<>=-])([\d+]\.?)+", "*", stdout)
+    stdout = re.sub(r"(?<=[<>=_-])[\d+](\.?_?[\d+])*", "*", stdout)
     stdout = re.sub(r" /[a-zA-Z0-9/]*/dist", " .../dist", stdout)
 
     return stdout.strip()
@@ -254,7 +254,7 @@ Successfully installed regex-2.0
         )
         == """\
 Looking in links: .../dist
-Processing ./dist/regex-*-cp310-cp310-emscripten_3_1_20_wasm32.whl
+Processing ./dist/regex-*-cp310-cp310-emscripten_*_wasm32.whl
 Installing collected packages: regex
 Successfully installed regex-*\
 """
@@ -356,7 +356,7 @@ def test_pip_install_from_pyodide(selenium, venv):
         == dedent(
             """
             Looking in links: .../dist
-            Processing ./dist/regex-*-cp310-cp310-emscripten_3_1_20_wasm32.whl
+            Processing ./dist/regex-*-cp310-cp310-emscripten_*_wasm32.whl
             Installing collected packages: regex
             Successfully installed regex-*
             """