diff --git a/src/plugins/intel_gpu/tests/functional/behavior/infer_request.cpp b/src/plugins/intel_gpu/tests/functional/behavior/infer_request.cpp
index af4fa65de6e54e..cb59e15b2dcd68 100644
--- a/src/plugins/intel_gpu/tests/functional/behavior/infer_request.cpp
+++ b/src/plugins/intel_gpu/tests/functional/behavior/infer_request.cpp
@@ -339,6 +339,10 @@ TEST(VariablesTest, smoke_padded_tensor_set_get_state_with_convert) {
 }
 
 TEST(TensorTest, smoke_outputTensorShapesForDynamicInput) {
+    // Issue: 126388
+    #if defined(_WIN32)
+        GTEST_SKIP();
+    #endif
     auto core = ov::Core();
     using namespace ov::preprocess;
     auto p = PrePostProcessor(ov::test::utils::make_split_multi_conv_concat());
diff --git a/src/plugins/intel_gpu/tests/functional/shared_tests_instances/skip_tests_config.cpp b/src/plugins/intel_gpu/tests/functional/shared_tests_instances/skip_tests_config.cpp
index 26b34f045daa08..91da6709aefb70 100644
--- a/src/plugins/intel_gpu/tests/functional/shared_tests_instances/skip_tests_config.cpp
+++ b/src/plugins/intel_gpu/tests/functional/shared_tests_instances/skip_tests_config.cpp
@@ -193,6 +193,8 @@ std::vector<std::string> disabledTestPatterns() {
             // by calc abs_threshold with expected value
             R"(.*smoke_RemoteTensor/OVRemoteTensorBatched_Test.NV12toBGR_buffer/(num_batch_4|num_batch_2).*)",
             R"(.*smoke_Check/ConstantResultSubgraphTest.Inference/SubgraphType=SINGLE_COMPONENT_IS=\[1,3,10,10\]_IT=i16_Device=GPU.*)",
+            // Issue: 126388
+            R"(.*smoke_outputTensorShapesForDynamicInput.*)",
 #endif
     };
     if (!isGPU1Present()) {