diff --git a/pkgs/development/libraries/xgboost/default.nix b/pkgs/development/libraries/xgboost/default.nix
index 24c6ec0635d..b4d668d5fba 100644
--- a/pkgs/development/libraries/xgboost/default.nix
+++ b/pkgs/development/libraries/xgboost/default.nix
@@ -43,6 +43,12 @@ stdenv.mkDerivation rec {
 
   inherit doCheck;
 
+  # By default, cmake build will run ctests with all checks enabled
+  # If we're building with cuda, we run ctest manually so that we can skip the GPU tests
+  checkPhase = lib.optionalString cudaSupport ''
+    ctest --force-new-ctest-process ${lib.optionalString cudaSupport "-E TestXGBoostLib"}
+  '';
+
   installPhase = let
     libname = "libxgboost${stdenv.hostPlatform.extensions.sharedLibrary}";
   in ''