diff --git a/src/plugins/intel_gpu/src/kernel_selector/CMakeLists.txt b/src/plugins/intel_gpu/src/kernel_selector/CMakeLists.txt
index 9437caf0815315..994ff994df2560 100644
--- a/src/plugins/intel_gpu/src/kernel_selector/CMakeLists.txt
+++ b/src/plugins/intel_gpu/src/kernel_selector/CMakeLists.txt
@@ -126,6 +126,10 @@ target_link_libraries(${TARGET_NAME} PUBLIC OpenCL::OpenCL openvino::runtime PRI
 
 target_include_directories(${TARGET_NAME} PRIVATE $<TARGET_PROPERTY:rapidjson,INTERFACE_INCLUDE_DIRECTORIES>)
 
+if (ENABLE_ONEDNN_FOR_GPU)
+  target_include_directories(${TARGET_NAME} PRIVATE $<TARGET_PROPERTY:onednn_gpu_tgt,INTERFACE_INTERNAL_INCLUDE_DIRECTORIES>)
+endif()
+
 set_target_properties(${TARGET_NAME} PROPERTIES INTERPROCEDURAL_OPTIMIZATION_RELEASE ${ENABLE_LTO})
 
 if(WIN32)
diff --git a/src/plugins/intel_gpu/src/runtime/CMakeLists.txt b/src/plugins/intel_gpu/src/runtime/CMakeLists.txt
index ddccadfa338625..e9f2581e81c01d 100644
--- a/src/plugins/intel_gpu/src/runtime/CMakeLists.txt
+++ b/src/plugins/intel_gpu/src/runtime/CMakeLists.txt
@@ -56,7 +56,8 @@ if(OV_COMPILER_IS_INTEL_LLVM)
 endif()
 
 if(ENABLE_ONEDNN_FOR_GPU)
-  ov_target_link_libraries_as_system(${TARGET_NAME} PUBLIC onednn_gpu_tgt)
+  ov_target_link_libraries_as_system(${TARGET_NAME} PRIVATE onednn_gpu_tgt)
+  target_include_directories(${TARGET_NAME} SYSTEM PRIVATE $<TARGET_PROPERTY:onednn_gpu_tgt,INTERFACE_INTERNAL_INCLUDE_DIRECTORIES>)
 endif()
 
 ov_set_threading_interface_for(${TARGET_NAME})
diff --git a/src/plugins/intel_gpu/src/runtime/ocl/ocl_device.cpp b/src/plugins/intel_gpu/src/runtime/ocl/ocl_device.cpp
index fd11298495f30a..7f929e0b268b1e 100644
--- a/src/plugins/intel_gpu/src/runtime/ocl/ocl_device.cpp
+++ b/src/plugins/intel_gpu/src/runtime/ocl/ocl_device.cpp
@@ -6,7 +6,7 @@
 #ifndef NOMINMAX
 # define NOMINMAX
 #endif
-#include "gpu/intel/jit/jit_generator.hpp"
+#include "gpu/intel/jit/generator.hpp"
 #endif  // ENABLE_ONEDNN_FOR_GPU
 
 #include "ocl_device.hpp"
@@ -324,7 +324,7 @@ device_info init_device_info(const cl::Device& device, const cl::Context& contex
     using namespace dnnl::impl::gpu::intel::jit;
     ngen::HW hw = ngen::HW::Unknown;
     ngen::Product product = {ngen::ProductFamily::Unknown, 0};
-    jit_generator<ngen::HW::Unknown>::detectHWInfo(context.get(), device.get(), hw, product);
+    generator_t<ngen::HW::Unknown>::detectHWInfo(context.get(), device.get(), hw, product);
     info.arch = convert_ngen_arch(hw);
     // We change the value of this flag to avoid OneDNN usage for the platforms unknown to OneDNN
     // This is required to guarantee some level of forward compatibility for the new HW generations
diff --git a/src/plugins/intel_gpu/thirdparty/CMakeLists.txt b/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
index 03956fcbd33012..0c4ff6f8068d02 100644
--- a/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
+++ b/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
@@ -156,25 +156,25 @@ if(ENABLE_ONEDNN_FOR_GPU)
             )
         endif()
 
-        set(LIB_INCLUDE_DIRS "${ONEDNN_INSTALL_DIR}/include" "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src")
+        set(LIB_INCLUDE_DIRS "${ONEDNN_INSTALL_DIR}/include")
+        set(LIB_INTERNAL_INCLUDE_DIRS "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src/"
+                                      "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src/gpu/intel/jit/ngen/"
+                                      "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/third_party/ngen/"
+                                      "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/third_party/")
         set(LIB_DEFINITIONS ENABLE_ONEDNN_FOR_GPU
                             DNNL_DLL
                             DNNL_DLL_EXPORTS
                             DNNL_ENABLE_CPU_ISA_HINTS
                             DNNL_ENABLE_MAX_CPU_ISA
-                            DNNL_X64=1
-                            NGEN_CPP11
-                            NGEN_NEO_INTERFACE
-                            NGEN_NO_OP_NAMES
-                            NGEN_SAFE
-                            NGEN_WINDOWS_COMPAT)
+                            DNNL_X64=1)
         add_library(onednn_gpu_tgt INTERFACE)
         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}"
-        )
+            INTERFACE_INTERNAL_INCLUDE_DIRECTORIES "${LIB_INTERNAL_INCLUDE_DIRS}"
+            )
         add_dependencies(onednn_gpu_tgt onednn_gpu_build)
 
         if(NOT BUILD_SHARED_LIBS)
diff --git a/src/plugins/intel_gpu/thirdparty/onednn_gpu b/src/plugins/intel_gpu/thirdparty/onednn_gpu
index 1584b5a36b8512..a6fd9524831910 160000
--- a/src/plugins/intel_gpu/thirdparty/onednn_gpu
+++ b/src/plugins/intel_gpu/thirdparty/onednn_gpu
@@ -1 +1 @@
-Subproject commit 1584b5a36b851265d59bd723abc235e13759be2f
+Subproject commit a6fd95248319105892f2afc53fe8924d9419ad42