diff --git a/pkgs/applications/science/logic/why3/configure.patch b/pkgs/applications/science/logic/why3/configure.patch
deleted file mode 100644
index 3eebf3cf165d1..0000000000000
--- a/pkgs/applications/science/logic/why3/configure.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff --git a/configure b/configure
---- a/configure
-+++ b/configure
-@@ -4029,7 +4029,6 @@ fi
- 
- if test "$USEOCAMLFIND" = yes; then
-    OCAMLFINDLIB=$(ocamlfind printconf stdlib)
--   OCAMLFIND=$(which ocamlfind)
-    if test "$OCAMLFINDLIB" != "$OCAMLLIB"; then
-    USEOCAMLFIND=no;
-    echo "but your ocamlfind is not compatible with your ocamlc:"
diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix
index cd44dadcedce8..b9bd2172bb1c4 100644
--- a/pkgs/applications/science/logic/why3/default.nix
+++ b/pkgs/applications/science/logic/why3/default.nix
@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation {
   pname = "why3";
-  version = "1.2.1";
+  version = "1.3.1";
 
   src = fetchurl {
-    url = "https://gforge.inria.fr/frs/download.php/file/38185/why3-1.2.1.tar.gz";
-    sha256 = "014gkwisjp05x3342zxkryb729p02ngx1hcjjsrplpa53jzgz647";
+    url = "https://gforge.inria.fr/frs/download.php/file/38291/why3-1.3.1.tar.gz";
+    sha256 = "16zcrc60zz2j3gd3ww93z2z9x2jkxb3kr57y8i5rcgmacy7mw3bv";
   };
 
   buildInputs = with ocamlPackages; [
@@ -29,15 +29,6 @@ stdenv.mkDerivation {
 
   enableParallelBuilding = true;
 
-  # Remove unnecessary call to which
-  patches = [ ./configure.patch
-    # Compatibility with js_of_ocaml 3.5
-    (fetchpatch {
-      url = "https://gitlab.inria.fr/why3/why3/commit/269ab313382fe3e64ef224813937314748bf7cf0.diff";
-      sha256 = "0i92wdnbh8pihvl93ac0ma1m5g95jgqqqj4kw6qqvbbjjqdgvzwa";
-    })
-  ];
-
   postPatch = ''
     substituteInPlace Makefile.in --replace js_of_ocaml.ppx js_of_ocaml-ppx
   '';