diff --git a/pkgs/development/python-modules/Cython/default.nix b/pkgs/development/python-modules/Cython/default.nix
index f4e8c927ad88..4f4cfea37c34 100644
--- a/pkgs/development/python-modules/Cython/default.nix
+++ b/pkgs/development/python-modules/Cython/default.nix
@@ -74,6 +74,10 @@ in buildPythonPackage rec {
   doCheck = false;
   # doCheck = !stdenv.isDarwin;
 
+  # force regeneration of generated code in source distributions
+  # https://github.com/cython/cython/issues/5089
+  setupHook = ./setup-hook.sh;
+
   meta = {
     changelog = "https://github.com/cython/cython/blob/${version}/CHANGES.rst";
     description = "An optimising static compiler for both the Python programming language and the extended Cython programming language";
diff --git a/pkgs/development/python-modules/Cython/setup-hook.sh b/pkgs/development/python-modules/Cython/setup-hook.sh
new file mode 100644
index 000000000000..c26330a53644
--- /dev/null
+++ b/pkgs/development/python-modules/Cython/setup-hook.sh
@@ -0,0 +1,3 @@
+if [ -z "${dontForceRegenCython-}"]; then
+  export CYTHON_FORCE_REGEN=1
+fi