diff --git a/cmake/onnxruntime_providers.cmake b/cmake/onnxruntime_providers.cmake
index ad46a0e07e..905f50f99b 100644
--- a/cmake/onnxruntime_providers.cmake
+++ b/cmake/onnxruntime_providers.cmake
@@ -1101,7 +1101,7 @@ if (onnxruntime_USE_QNN)
   add_dependencies(onnxruntime_providers_qnn onnx ${onnxruntime_EXTERNAL_DEPENDENCIES})
   set_target_properties(onnxruntime_providers_qnn PROPERTIES CXX_STANDARD_REQUIRED ON)
   set_target_properties(onnxruntime_providers_qnn PROPERTIES FOLDER "ONNXRuntime")
-  target_include_directories(onnxruntime_providers_qnn PRIVATE ${ONNXRUNTIME_ROOT} ${onnxruntime_QNN_HOME}/include)
+  target_include_directories(onnxruntime_providers_qnn PRIVATE ${ONNXRUNTIME_ROOT} ${onnxruntime_QNN_HOME}/include/QNN ${onnxruntime_QNN_HOME}/include)
   set_target_properties(onnxruntime_providers_qnn PROPERTIES LINKER_LANGUAGE CXX)
   # ignore the warning unknown-pragmas on "pragma region"
   if(NOT MSVC)
diff --git a/cmake/onnxruntime_unittests.cmake b/cmake/onnxruntime_unittests.cmake
index aa00e02145..1fd09ab493 100644
--- a/cmake/onnxruntime_unittests.cmake
+++ b/cmake/onnxruntime_unittests.cmake
@@ -920,9 +920,9 @@ if (NOT onnxruntime_ENABLE_TRAINING_TORCH_INTEROP)
     endif()
 
     if (MSVC OR ${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
-        file(GLOB QNN_LIB_FILES LIST_DIRECTORIES false "${onnxruntime_QNN_HOME}/target/${QNN_ARCH_ABI}/lib/*.so" "${onnxruntime_QNN_HOME}/target/${QNN_ARCH_ABI}/lib/*.dll")
+        file(GLOB QNN_LIB_FILES LIST_DIRECTORIES false "${onnxruntime_QNN_HOME}/lib/${QNN_ARCH_ABI}/*.so" "${onnxruntime_QNN_HOME}/target/${QNN_ARCH_ABI}/lib/*.so" "${onnxruntime_QNN_HOME}/lib/${QNN_ARCH_ABI}/*.dll" "${onnxruntime_QNN_HOME}/target/${QNN_ARCH_ABI}/lib/*.dll")
         if (${QNN_ARCH_ABI} STREQUAL "aarch64-windows-msvc")
-          file(GLOB EXTRA_HTP_LIB LIST_DIRECTORIES false "${onnxruntime_QNN_HOME}/target/hexagon-v68/lib/unsigned/libQnnHtpV68Skel.so")
+          file(GLOB EXTRA_HTP_LIB LIST_DIRECTORIES false "${onnxruntime_QNN_HOME}/lib/hexagon-v68/unsigned/libQnnHtpV68Skel.so" "${onnxruntime_QNN_HOME}/target/hexagon-v68/lib/unsigned/libQnnHtpV68Skel.so")
           list(APPEND QNN_LIB_FILES ${EXTRA_HTP_LIB})
         endif()
         message(STATUS "QNN lib files: " ${QNN_LIB_FILES})