diff --git a/pkgs/development/tools/build-managers/cmake/setup-hook.sh b/pkgs/development/tools/build-managers/cmake/setup-hook.sh
index eaabb37f4987..f6dd5460c352 100755
--- a/pkgs/development/tools/build-managers/cmake/setup-hook.sh
+++ b/pkgs/development/tools/build-managers/cmake/setup-hook.sh
@@ -70,15 +70,25 @@ else
 fi
 
 makeCmakeFindLibs(){
+  isystem_seen=
   for flag in $NIX_CFLAGS_COMPILE $NIX_LDFLAGS; do
-    case $flag in
-      -I*)
-        export CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH${CMAKE_INCLUDE_PATH:+:}${flag:2}"
-        ;;
-      -L*)
-        export CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH${CMAKE_LIBRARY_PATH:+:}${flag:2}"
-        ;;
-    esac
+    if test -n "$isystem_seen" && test -d "$flag"; then
+      isystem_seen=
+      export CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH${CMAKE_INCLUDE_PATH:+:}${flag}"
+    else
+      isystem_seen=
+      case $flag in
+        -I*)
+          export CMAKE_INCLUDE_PATH="$CMAKE_INCLUDE_PATH${CMAKE_INCLUDE_PATH:+:}${flag:2}"
+          ;;
+        -L*)
+          export CMAKE_LIBRARY_PATH="$CMAKE_LIBRARY_PATH${CMAKE_LIBRARY_PATH:+:}${flag:2}"
+          ;;
+        -isystem)
+          isystem_seen=1
+          ;;
+      esac
+    fi
   done
 }