diff --git a/pkgs/development/libraries/fplll/default.nix b/pkgs/development/libraries/fplll/default.nix
index 829117adf8c..694b6d567eb 100644
--- a/pkgs/development/libraries/fplll/default.nix
+++ b/pkgs/development/libraries/fplll/default.nix
@@ -1,5 +1,6 @@
 { stdenv
 , fetchFromGitHub
+, fetchpatch
 , gettext
 , autoreconfHook
 , gmp
@@ -8,15 +9,24 @@
 
 stdenv.mkDerivation rec {
   pname = "fplll";
-  version = "5.2.1";
+  version = "5.3.0";
 
   src = fetchFromGitHub {
     owner = "fplll";
     repo = "fplll";
     rev = version;
-    sha256 = "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg";
+    sha256 = "0wxa4xs7as7y47h7i6prmk5r0srabdvrlkvza3j50pixir5swgvh";
   };
 
+  patches = [
+    # https://github.com/fplll/fpylll/issues/161
+    (fetchpatch {
+      name = "fix-out-of-bounds-access.patch";
+      url = "https://github.com/fplll/fplll/pull/398/commits/f68e257228bf073ef380f996326d02197ce7b0e4.patch";
+      sha256 = "1rapkcf389lf579va6kbnvhzyv36n4l4d9n0vg2zxprvql8wvm7m";
+    })
+  ];
+
   nativeBuildInputs = [
     gettext
     autoreconfHook
diff --git a/pkgs/development/python-modules/fpylll/default.nix b/pkgs/development/python-modules/fpylll/default.nix
index a27e9494911..3236a3de16f 100644
--- a/pkgs/development/python-modules/fpylll/default.nix
+++ b/pkgs/development/python-modules/fpylll/default.nix
@@ -14,13 +14,13 @@
 
 buildPythonPackage rec {
   pname = "fpylll";
-  version = "0.4.1dev";
+  version = "0.5.0dev";
 
   src = fetchFromGitHub {
     owner = "fplll";
     repo = "fpylll";
     rev = version;
-    sha256 = "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w";
+    sha256 = "091zqgsqd5cqma1hvimkq5xpr9f1jw80v9m2fr6k9hvssqjzgnab";
   };
 
   buildInputs = [
@@ -45,7 +45,11 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    py.test
+    # Since upstream introduced --doctest-modules in
+    # https://github.com/fplll/fpylll/commit/9732fdb40cf1bd43ad1f60762ec0a8401743fc79,
+    # it is necessary to ignore import mismatches. Not sure why, but the files
+    # should be identical anyway.
+    PY_IGNORE_IMPORTMISMATCH=1 pytest
   '';
 
   meta = {