diff --git a/pkgs/by-name/cm/cmdstan/package.nix b/pkgs/by-name/cm/cmdstan/package.nix
index d490a39095c6..a8195d92855d 100644
--- a/pkgs/by-name/cm/cmdstan/package.nix
+++ b/pkgs/by-name/cm/cmdstan/package.nix
@@ -12,19 +12,19 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "cmdstan";
-  version = "2.38.0";
+  version = "2.39.0";
 
   src = fetchFromGitHub {
     owner = "stan-dev";
     repo = "cmdstan";
     tag = "v${finalAttrs.version}";
     fetchSubmodules = true;
-    hash = "sha256-4Mx4LvXW2lYOSSOgNT0f+unry6mBobgGTDLwtiypHBU=";
+    hash = "sha256-7vGEqIJOFWeESq4xL2z2ZjNaVWEqqzPmGT6tpWBzrU0=";
   };
 
   postPatch = ''
     substituteInPlace stan/lib/stan_math/make/libraries \
-      --replace "/usr/bin/env bash" "bash"
+      --replace-fail "/usr/bin/env bash" "bash"
   '';
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/st/stanc/package.nix b/pkgs/by-name/st/stanc/package.nix
index 0bad4160a49b..f2a82d21680a 100644
--- a/pkgs/by-name/st/stanc/package.nix
+++ b/pkgs/by-name/st/stanc/package.nix
@@ -6,7 +6,7 @@
 
 ocamlPackages.buildDunePackage rec {
   pname = "stanc";
-  version = "2.38.0";
+  version = "2.39.0";
 
   minimalOCamlVersion = "4.12";
 
@@ -14,7 +14,7 @@ ocamlPackages.buildDunePackage rec {
     owner = "stan-dev";
     repo = "stanc3";
     tag = "v${version}";
-    hash = "sha256-j05PMQKIqkM9UWJzSVnkYWe6d+iUnmFOh1W8pZ7Fdyk=";
+    hash = "sha256-ZAH9uFEZu75BC2xYGUXg62RHiADmKYBYP2Nt8bwEVRY=";
   };
 
   nativeBuildInputs = with ocamlPackages; [
diff --git a/pkgs/development/python-modules/cmdstanpy/default.nix b/pkgs/development/python-modules/cmdstanpy/default.nix
index feda60658931..9a9f926df8fb 100644
--- a/pkgs/development/python-modules/cmdstanpy/default.nix
+++ b/pkgs/development/python-modules/cmdstanpy/default.nix
@@ -2,6 +2,7 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchpatch,
   replaceVars,
   cmdstan,
   setuptools,
@@ -30,6 +31,15 @@ buildPythonPackage (finalAttrs: {
     (replaceVars ./use-nix-cmdstan-path.patch {
       cmdstan = "${cmdstan}/opt/cmdstan";
     })
+    # Fix tests for cmdstan 2.39.0
+    (fetchpatch {
+      url = "https://github.com/stan-dev/cmdstanpy/commit/5ef72db67660b8fb0ea0ba25bef9667e88aafc5f.patch";
+      hash = "sha256-BZcJiRAluItsfzvGJ2yJVDHuUp92AI19x7d06wRGzY4=";
+    })
+    (fetchpatch {
+      url = "https://github.com/stan-dev/cmdstanpy/commit/f08c69835d2d4a69c7e526d939757b8f609da8f6.patch";
+      hash = "sha256-3o8d5h0eRkghav2vuG6eERf6u6GJSKEaqmnGhfBXbjk=";
+    })
   ];
 
   postPatch = ''