diff --git a/Makefile.envs b/Makefile.envs
index e9c16a425..8b9345f0a 100644
--- a/Makefile.envs
+++ b/Makefile.envs
@@ -1,5 +1,5 @@
 export PYVERSION ?= 3.11.3
-export PYODIDE_EMSCRIPTEN_VERSION ?= 3.1.39
+export PYODIDE_EMSCRIPTEN_VERSION ?= 3.1.40
 
 ifdef CPYTHON_DEBUG
 	export CPYTHON_ABI_FLAGS=d
diff --git a/docs/project/changelog.md b/docs/project/changelog.md
index 3d35be731..dda904166 100644
--- a/docs/project/changelog.md
+++ b/docs/project/changelog.md
@@ -35,8 +35,8 @@ myst:
 - {{ Enhancement }} Make it possible to use the @example JSDoc directive.
   {pr}`4009`
 
-- {{ Enhancement }} ABI Break: Updated Emscripten to version 3.1.39
-  {pr}`3665`, {pr}`3659`, {pr}`3822`, {pr}`3889`, {pr}`3890`
+- {{ Enhancement }} ABI Break: Updated Emscripten to version 3.1.40
+  {pr}`3665`, {pr}`3659`, {pr}`3822`, {pr}`3889`, {pr}`3890`, {pr}`3888`
 
 - {{ Update }} The docker image now has node v20 instead of node v14.
   {pr}`3819`
diff --git a/emsdk/patches/0001-Fix-fcntl-DUPFD.patch b/emsdk/patches/0001-Fix-fcntl-DUPFD.patch
new file mode 100644
index 000000000..bf1b973d4
--- /dev/null
+++ b/emsdk/patches/0001-Fix-fcntl-DUPFD.patch
@@ -0,0 +1,79 @@
+From b3b02ec173471bfb541da23d396c9644a7187cef Mon Sep 17 00:00:00 2001
+From: Hood Chatham <roberthoodchatham@gmail.com>
+Date: Mon, 7 Aug 2023 16:29:04 +0200
+Subject: [PATCH] Fix fcntl DUPFD
+
+Backport of Emscripten PR 19986:
+https://github.com/emscripten-core/emscripten/pull/19986
+
+PR #19391 introduced a regression in fcntl F_DUPFD. In particular, the manpage for
+fcntl says it should:
+
+> Duplicate the file descriptor fd using the lowest-numbered available file descriptor
+> greater than or equal to arg.
+
+But now it uses fd exactly arg, even if this fd already exists. This pretty badly
+screws up file system state.
+---
+ src/library_syscall.js    |  3 +++
+ test/fcntl/test_fcntl.c   | 12 ++++++++++--
+ test/fcntl/test_fcntl.out |  8 +++++++-
+ 3 files changed, 20 insertions(+), 3 deletions(-)
+
+diff --git a/src/library_syscall.js b/src/library_syscall.js
+index 3ccf03781..ab9b8ac20 100644
+--- a/src/library_syscall.js
++++ b/src/library_syscall.js
+@@ -752,6 +752,9 @@ var SyscallsLibrary = {
+         if (arg < 0) {
+           return -{{{ cDefs.EINVAL }}};
+         }
++        while (FS.streams[arg]) {
++          arg++;
++        }
+         var newStream;
+         newStream = FS.createStream(stream, arg);
+         return newStream.fd;
+diff --git a/test/fcntl/test_fcntl.c b/test/fcntl/test_fcntl.c
+index 0f531c284..3839f7ef9 100644
+--- a/test/fcntl/test_fcntl.c
++++ b/test/fcntl/test_fcntl.c
+@@ -12,9 +12,17 @@
+ 
+ int main() {
+   int f = open("test", O_RDWR, 0777);
+-  assert(f > 0);
++  assert(f == 3);
+ 
+-  printf("F_DUPFD: %d\n", fcntl(f, F_DUPFD, 100) >= 100);
++  printf("F_DUPFD 1: %d\n", fcntl(f, F_DUPFD, 0) == 4);
++  printf("errno: %d\n", errno);
++  printf("\n");
++
++  printf("F_DUPFD 2: %d\n", fcntl(f, F_DUPFD, 100) == 100);
++  printf("errno: %d\n", errno);
++  printf("\n");
++
++  printf("F_DUPFD_CLOEXEC: %d\n", fcntl(f, F_DUPFD_CLOEXEC, 0) == 5);
+   printf("errno: %d\n", errno);
+   printf("\n");
+   errno = 0;
+diff --git a/test/fcntl/test_fcntl.out b/test/fcntl/test_fcntl.out
+index b0d458c24..6192b8558 100644
+--- a/test/fcntl/test_fcntl.out
++++ b/test/fcntl/test_fcntl.out
+@@ -1,4 +1,10 @@
+-F_DUPFD: 1
++F_DUPFD 1: 1
++errno: 0
++
++F_DUPFD 2: 1
++errno: 0
++
++F_DUPFD_CLOEXEC: 1
+ errno: 0
+ 
+ F_DUPFD/error1: -1
+-- 
+2.25.1
+