diff --git a/pkgs/development/python-modules/pyjwt/default.nix b/pkgs/development/python-modules/pyjwt/default.nix
index f7d3e32f992..94a1a4e6b0e 100644
--- a/pkgs/development/python-modules/pyjwt/default.nix
+++ b/pkgs/development/python-modules/pyjwt/default.nix
@@ -15,6 +15,13 @@ buildPythonPackage rec {
 
   checkInputs = [ pytestrunner pytestcov pytest ];
 
+  # pytest 3.9.0 changed behavior of deprecated_call, see release notes
+  postPatch = ''
+    for x in tests/test_api_*py; do
+      substituteInPlace "$x" --replace AssertionError pytest.fail.Exception
+    done
+  '';
+
   meta = with lib; {
     description = "JSON Web Token implementation in Python";
     homepage = https://github.com/jpadilla/pyjwt;