diff --git a/src/plugins/intel_gpu/src/kernel_selector/micro_utils.hpp b/src/plugins/intel_gpu/src/kernel_selector/micro_utils.hpp
index 15c60862da1c23..160325c1f9921b 100644
--- a/src/plugins/intel_gpu/src/kernel_selector/micro_utils.hpp
+++ b/src/plugins/intel_gpu/src/kernel_selector/micro_utils.hpp
@@ -18,7 +18,7 @@
 #endif
 
 #include "gpu/intel/microkernels/package.hpp"
-#include "gpu/intel/jit/gemm/include/gemmstone/microkernel_provider.hpp"
+#include "gpu/intel/gemm/jit/include/gemmstone/microkernel_provider.hpp"
 #include "gpu/intel/microkernels/shim.hpp"
 #include "common/utils.hpp"
 
diff --git a/src/plugins/intel_gpu/thirdparty/CMakeLists.txt b/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
index e47b2b1ffdbb3a..b9a904a03f6271 100644
--- a/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
+++ b/src/plugins/intel_gpu/thirdparty/CMakeLists.txt
@@ -160,7 +160,7 @@ if(ENABLE_ONEDNN_FOR_GPU)
                              "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src"
                              "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src/gpu/intel/jit/ngen"
                              "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src/gpu/intel/jit/config"
-                             "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src/gpu/intel/jit/gemm/include"
+                             "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/src/gpu/intel/gemm/jit/include"
                              "${CMAKE_CURRENT_SOURCE_DIR}/onednn_gpu/third_party/ngen")
         set(LIB_DEFINITIONS ENABLE_ONEDNN_FOR_GPU
                             DNNL_DLL
diff --git a/src/plugins/intel_gpu/thirdparty/onednn_gpu b/src/plugins/intel_gpu/thirdparty/onednn_gpu
index 8edf6bb60fdaa2..d8fb6faac0418b 160000
--- a/src/plugins/intel_gpu/thirdparty/onednn_gpu
+++ b/src/plugins/intel_gpu/thirdparty/onednn_gpu
@@ -1 +1 @@
-Subproject commit 8edf6bb60fdaa2769f3cebf44bd2ee94da00744c
+Subproject commit d8fb6faac0418b03a598d8f6aaaa865610ff9f40