diff --git a/pkgs/by-name/pi/pinocchio/package.nix b/pkgs/by-name/pi/pinocchio/package.nix
index 54e35f5775bea..5144a6af25014 100644
--- a/pkgs/by-name/pi/pinocchio/package.nix
+++ b/pkgs/by-name/pi/pinocchio/package.nix
@@ -1,33 +1,43 @@
 {
+  lib,
+
+  fetchFromGitHub,
+  nix-update-script,
+  stdenv,
+
+  # nativeBuildInputs
+  cmake,
+  doxygen,
+  pkg-config,
+
+  # propagatedBuildInputs
   boost,
   casadi,
-  casadiSupport ? true,
-  cmake,
-  collisionSupport ? true,
+  coal,
   console-bridge,
-  ctestCheckHook,
-  doxygen,
   eigen,
-  example-robot-data,
-  fetchFromGitHub,
-  fetchpatch,
-  coal,
   jrl-cmakemodules,
-  lib,
-  pkg-config,
-  stdenv,
   urdfdom,
+
+  # nativeCheckInputs
+  ctestCheckHook,
+
+  # checkInputs = [
+  example-robot-data,
+
+  casadiSupport ? true,
+  collisionSupport ? true,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "pinocchio";
-  version = "3.8.0";
+  version = "3.9.0";
 
   src = fetchFromGitHub {
     owner = "stack-of-tasks";
     repo = "pinocchio";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-2oMP653fJ7Msk+IB8whRk2L8xkAmRdDeMLPJyyD99OQ=";
+    hash = "sha256-k2lT1I0wb3N/o95ol2oO6HSYHf4wKJ0SFEg8JNxZmpI=";
   };
 
   outputs = [
@@ -35,19 +45,7 @@ stdenv.mkDerivation (finalAttrs: {
     "doc"
   ];
 
-  patches = [
-    # ref. https://github.com/stack-of-tasks/pinocchio/pull/2771
-    (fetchpatch {
-      name = "fix-viser-path.patch";
-      url = "https://github.com/stack-of-tasks/pinocchio/commit/36a04bddb6980a7bcd28ebcc55d4e442f7920d87.patch";
-      hash = "sha256-9oENiMmRqJLU4ZiyGojm7suqdwTDGfk56aS2kcZiGaI=";
-    })
-  ];
-
   postPatch = ''
-    # allow package:// uri use in examples
-    export ROS_PACKAGE_PATH=${example-robot-data}/share
-
     # silence matplotlib warning
     export MPLCONFIGDIR=$(mktemp -d)
   '';
@@ -99,9 +97,12 @@ stdenv.mkDerivation (finalAttrs: {
 
   doCheck = true;
 
+  passthru.updateScript = nix-update-script { };
+
   meta = {
     description = "Fast and flexible implementation of Rigid Body Dynamics algorithms and their analytical derivatives";
     homepage = "https://github.com/stack-of-tasks/pinocchio";
+    changelog = "https://github.com/stack-of-tasks/pinocchio/blob/devel/CHANGELOG.md";
     license = lib.licenses.bsd2;
     maintainers = with lib.maintainers; [
       nim65s
diff --git a/pkgs/development/python-modules/pinocchio/default.nix b/pkgs/development/python-modules/pinocchio/default.nix
index 95bda9dc0959a..9044a4e3153bd 100644
--- a/pkgs/development/python-modules/pinocchio/default.nix
+++ b/pkgs/development/python-modules/pinocchio/default.nix
@@ -9,6 +9,7 @@
   coal,
   casadi,
   matplotlib,
+  pybind11,
   python,
 
   buildStandalone ? true,
@@ -35,6 +36,7 @@ toPythonModule (
 
     checkInputs = super.checkInputs ++ [
       matplotlib
+      pybind11
     ];
 
     nativeCheckInputs = super.nativeCheckInputs ++ [