diff --git a/src/plugins/intel_gpu/src/graph/CMakeLists.txt b/src/plugins/intel_gpu/src/graph/CMakeLists.txt
index b3ee51e242..31477ec128 100644
--- a/src/plugins/intel_gpu/src/graph/CMakeLists.txt
+++ b/src/plugins/intel_gpu/src/graph/CMakeLists.txt
@@ -82,7 +82,7 @@ macro(ov_gpu_add_backend_target)

     # We use onednn headers all over the graph module, so we have to append includes to all backends and add a dependency between targets
     if (ENABLE_ONEDNN_FOR_GPU)
-        target_include_directories(${ARG_NAME} SYSTEM BEFORE PRIVATE $<TARGET_PROPERTY:onednn_gpu_tgt,INTERFACE_INCLUDE_DIRECTORIES>)
+        target_include_directories(${ARG_NAME} BEFORE PRIVATE $<TARGET_PROPERTY:onednn_gpu_tgt,INTERFACE_INCLUDE_DIRECTORIES>)
         add_dependencies(openvino_intel_gpu_${IMPL_TYPE}_obj onednn_gpu_tgt)
     endif()
 endmacro()
diff --git a/src/plugins/intel_gpu/src/runtime/CMakeLists.txt b/src/plugins/intel_gpu/src/runtime/CMakeLists.txt
index 85dfec05c4..3f72a41949 100644
--- a/src/plugins/intel_gpu/src/runtime/CMakeLists.txt
+++ b/src/plugins/intel_gpu/src/runtime/CMakeLists.txt
@@ -56,7 +56,7 @@ if(OV_COMPILER_IS_INTEL_LLVM)
 endif()

 if(ENABLE_ONEDNN_FOR_GPU)
-  ov_target_link_libraries_as_system(${TARGET_NAME} PUBLIC onednn_gpu_tgt)
+  target_link_libraries(${TARGET_NAME} PUBLIC onednn_gpu_tgt)
 endif()

 ov_set_threading_interface_for(${TARGET_NAME})
diff --git a/src/plugins/intel_gpu/thirdparty/CMakeLists.txt b/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
index e47b2b1ffd..e03c95fdeb 100644
--- a/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
+++ b/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
@@ -173,7 +173,6 @@ if(ENABLE_ONEDNN_FOR_GPU)
         set_target_properties(onednn_gpu_tgt PROPERTIES
             INTERFACE_LINK_LIBRARIES $<BUILD_INTERFACE:${ONEDNN_GPU_LIB_PATH}>
             INTERFACE_INCLUDE_DIRECTORIES "$<BUILD_INTERFACE:${LIB_INCLUDE_DIRS}>"
-            INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "${LIB_INCLUDE_DIRS}"
             INTERFACE_COMPILE_DEFINITIONS "${LIB_DEFINITIONS}"
         )
         add_dependencies(onednn_gpu_tgt onednn_gpu_build)