diff --git a/pkgs/development/compilers/binaryen/0001-Get-rid-of-git-dependency.patch b/pkgs/development/compilers/binaryen/0001-Get-rid-of-git-dependency.patch
new file mode 100644
index 000000000000..79b053592a95
--- /dev/null
+++ b/pkgs/development/compilers/binaryen/0001-Get-rid-of-git-dependency.patch
@@ -0,0 +1,38 @@
+From 1c6af6c68ba3f49ae9e942844c739e934339d3b9 Mon Sep 17 00:00:00 2001
+From: Maximilian Bosch <maximilian@mbosch.me>
+Date: Sat, 14 Mar 2020 00:37:31 +0100
+Subject: [PATCH] Get rid of git dependency
+
+---
+ CMakeLists.txt | 15 +--------------
+ 1 file changed, 1 insertion(+), 14 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 4acf703e1..4e9bd60b5 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -7,20 +7,7 @@ IF(NOT CMAKE_BUILD_TYPE)
+   SET(CMAKE_BUILD_TYPE "Release")
+ ENDIF()
+ 
+-FIND_PACKAGE(Git QUIET REQUIRED)
+-EXECUTE_PROCESS(COMMAND
+-             "${GIT_EXECUTABLE}" --git-dir=${CMAKE_CURRENT_SOURCE_DIR}/.git describe --tags
+-         RESULT_VARIABLE
+-             GIT_HASH_RESULT
+-         OUTPUT_VARIABLE
+-             GIT_HASH
+-         OUTPUT_STRIP_TRAILING_WHITESPACE)
+-IF(${GIT_HASH_RESULT})
+-  MESSAGE(WARNING "Error running git describe to determine version")
+-  SET(BINARYEN_VERSION_INFO "(unable to determine version)")
+-ELSE()
+-  SET(BINARYEN_VERSION_INFO "${GIT_HASH}")
+-ENDIF()
++SET(BINARYEN_VERSION_INFO "@emscriptenv@")
+ CONFIGURE_FILE(config.h.in config.h)
+ 
+ OPTION(BUILD_STATIC_LIB "Build as a static library" OFF)
+-- 
+2.25.0
+
diff --git a/pkgs/development/compilers/binaryen/default.nix b/pkgs/development/compilers/binaryen/default.nix
index 664335c3dade..d37232437668 100644
--- a/pkgs/development/compilers/binaryen/default.nix
+++ b/pkgs/development/compilers/binaryen/default.nix
@@ -1,12 +1,12 @@
-{ stdenv, cmake, python, fetchFromGitHub, emscriptenRev ? null }:
+{ stdenv, cmake, python3, fetchFromGitHub, emscriptenRev ? null, substituteAll }:
 
 let
-  defaultVersion = "89";
+  defaultVersion = "91";
 
   # Map from git revs to SHA256 hashes
   sha256s = {
-    version_89 = "0rh1dq33ilq54szfgi1ajaiaj7rbylai02rhp9zm9vpwp0rw8mij";
-    "1.38.28" = "172s7y5f38736ic8ri3mnbdqcrkadd40a26cxcfwbscc53phl11v";
+    version_91 = "1qsjqnzc5w9ny9v01bxkdvhh4kgbsia01x5vvac72m075v4mpgs4";
+    "1.39.1" = "0ygm9m5322h4vfpf3j63q32qxk2l26yk62hh7dkb49j51zwl1y3y";
   };
 in
 
@@ -29,7 +29,12 @@ stdenv.mkDerivation rec {
     inherit rev;
   };
 
-  nativeBuildInputs = [ cmake python ];
+  patches = stdenv.lib.optional (emscriptenRev != null) (substituteAll {
+    src = ./0001-Get-rid-of-git-dependency.patch;
+    emscriptenv = "1.39.1";
+  });
+
+  nativeBuildInputs = [ cmake python3 ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/WebAssembly/binaryen;
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 59aa969983bb..013d6d2559fe 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -3094,7 +3094,7 @@ in
 
   cholmod-extra = callPackage ../development/libraries/science/math/cholmod-extra { };
 
-  emscriptenVersion = "1.38.28";
+  emscriptenVersion = "1.39.1";
 
   emscripten = callPackage ../development/compilers/emscripten { };