diff --git a/include/onnxruntime/core/session/onnxruntime_session_options_config_keys.h b/include/onnxruntime/core/session/onnxruntime_session_options_config_keys.h
index efe628b354..018e1ddc81 100644
--- a/include/onnxruntime/core/session/onnxruntime_session_options_config_keys.h
+++ b/include/onnxruntime/core/session/onnxruntime_session_options_config_keys.h
@@ -275,6 +275,7 @@ static const char* const kOrtSessionOptionEpContextEnable = "ep.context_enable";
 
 // Specify the file path for the Onnx model which has EP context.
 // Default to original_file_name_ctx.onnx if not specified
+// Folder is not a valid option
 static const char* const kOrtSessionOptionEpContextFilePath = "ep.context_file_path";
 
 // Flag to specify whether to dump the EP context into the Onnx model.
diff --git a/onnxruntime/core/framework/graph_partitioner.cc b/onnxruntime/core/framework/graph_partitioner.cc
index 7c980a1aeb..c02e6cf3af 100644
--- a/onnxruntime/core/framework/graph_partitioner.cc
+++ b/onnxruntime/core/framework/graph_partitioner.cc
@@ -643,6 +643,29 @@ static Status InlineFunctionsAOTImpl(const ExecutionProviders& execution_provide
   return Status::OK();
 }
 
+// Validate the ep_context_path to make sure it is file path and check whether the file exist already
+static Status EpContextFilePathCheck(const std::string& ep_context_path,
+                                     const std::filesystem::path& model_path) {
+  std::filesystem::path context_cache_path;
+  if (!ep_context_path.empty()) {
+    context_cache_path = ep_context_path;
+    if (!context_cache_path.has_filename()) {
+      return ORT_MAKE_STATUS(ONNXRUNTIME, INVALID_ARGUMENT, "context_file_path should not point to a folder.");
+    }
+  } else if (!model_path.empty()) {
+    context_cache_path = model_path.native() + ORT_TSTR("_ctx.onnx");
+  } else {
+    return ORT_MAKE_STATUS(ONNXRUNTIME, INVALID_ARGUMENT, "Both ep_context_path and model_path are empty.");
+  }
+
+  if (std::filesystem::exists(context_cache_path)) {
+    return ORT_MAKE_STATUS(ONNXRUNTIME, FAIL, "Failed to generate EP context model since the file '",
+                           context_cache_path, "' exist already.");
+  }
+
+  return Status::OK();
+}
+
 static Status CreateEpContextModel(const ExecutionProviders& execution_providers,
                                    const Graph& graph,
                                    const std::filesystem::path& ep_context_path,
@@ -678,11 +701,6 @@ static Status CreateEpContextModel(const ExecutionProviders& execution_providers
     return ORT_MAKE_STATUS(ONNXRUNTIME, INVALID_ARGUMENT, "Both ep_context_path and model_path are empty");
   }
 
-  if (std::filesystem::exists(context_cache_path)) {
-    return ORT_MAKE_STATUS(ONNXRUNTIME, FAIL, "Failed to generate EP context model since the file '",
-                           context_cache_path, "' exist already.");
-  }
-
   Model ep_context_model(graph.Name(), false, graph.GetModel().MetaData(),
                          graph.GetModel().ModelPath(),  // use source model path so that external initializers can find the data file path
                          IOnnxRuntimeOpSchemaRegistryList{graph.GetSchemaRegistry()},
@@ -1007,9 +1025,15 @@ Status GraphPartitioner::Partition(Graph& graph, FuncManager& func_mgr,
 
   if (mode == Mode::kNormal || mode == Mode::kAssignOnly) {
 #if !defined(ORT_MINIMAL_BUILD)
+    bool ep_context_enabled = config_options.GetConfigOrDefault(kOrtSessionOptionEpContextEnable, "0") == "1";
+    if (ep_context_enabled) {
+      std::string ep_context_path = config_options.GetConfigOrDefault(kOrtSessionOptionEpContextFilePath, "");
+      // Check before EP compile graphs
+      ORT_RETURN_IF_ERROR(EpContextFilePathCheck(ep_context_path, graph.ModelPath()));
+    }
+
     ORT_RETURN_IF_ERROR(PartitionOnnxFormatModel(partition_params, mode, providers_, kernel_registry_mgr_, logger));
 
-    bool ep_context_enabled = config_options.GetConfigOrDefault(kOrtSessionOptionEpContextEnable, "0") == "1";
     if (ep_context_enabled) {
       std::string ep_context_path = config_options.GetConfigOrDefault(kOrtSessionOptionEpContextFilePath, "");
       std::string external_ini_file_name = config_options.GetConfigOrDefault(kOrtSessionOptionsEpContextModelExternalInitializersFileName, "");
diff --git a/onnxruntime/test/providers/qnn/qnn_ep_context_test.cc b/onnxruntime/test/providers/qnn/qnn_ep_context_test.cc
index 8670fbbe2b..29a916997b 100644
--- a/onnxruntime/test/providers/qnn/qnn_ep_context_test.cc
+++ b/onnxruntime/test/providers/qnn/qnn_ep_context_test.cc
@@ -252,6 +252,113 @@ TEST_F(QnnHTPBackendTests, QnnContextBinaryCpuNodeWithoutExternalWeights) {
   EpCtxCpuNodeWithExternalIniFileTestBody(false);
 }
 
+// Set ep.context_file_path to folder path which is not a valid option, check the error message
+TEST_F(QnnHTPBackendTests, QnnContextBinaryGenerationFolderPathNotExpected) {
+  ProviderOptions provider_options;
+#if defined(_WIN32)
+  provider_options["backend_path"] = "QnnHtp.dll";
+#else
+  provider_options["backend_path"] = "libQnnHtp.so";
+#endif
+  provider_options["offload_graph_io_quantization"] = "0";
+
+  const std::unordered_map<std::string, int> domain_to_version = {{"", 13}, {kMSDomain, 1}};
+
+  auto& logging_manager = DefaultLoggingManager();
+  logging_manager.SetDefaultLoggerSeverity(logging::Severity::kERROR);
+
+  onnxruntime::Model model("QNN_EP_TestModel", false, ModelMetaData(), PathString(),
+                           IOnnxRuntimeOpSchemaRegistryList(), domain_to_version, {},
+                           logging_manager.DefaultLogger());
+  Graph& graph = model.MainGraph();
+  ModelTestBuilder helper(graph);
+  bool single_ep_node = true;
+  BuildGraphWithQAndNonQ(single_ep_node)(helper);
+  helper.SetGraphOutputs();
+  ASSERT_STATUS_OK(model.MainGraph().Resolve());
+
+  // Serialize the model to a string.
+  std::string model_data;
+  model.ToProto().SerializeToString(&model_data);
+
+  const auto model_data_span = AsByteSpan(model_data.data(), model_data.size());
+
+  const std::string ep_context_onnx_file = "./ep_context_folder_not_expected/";
+  std::remove(ep_context_onnx_file.c_str());
+  Ort::SessionOptions so;
+  so.AddConfigEntry(kOrtSessionOptionEpContextEnable, "1");
+  so.AddConfigEntry(kOrtSessionOptionEpContextFilePath, ep_context_onnx_file.c_str());
+  so.AppendExecutionProvider("QNN", provider_options);
+
+  try {
+    Ort::Session session(*ort_env, model_data_span.data(), model_data_span.size(), so);
+    FAIL();  // Should not get here!
+  } catch (const Ort::Exception& excpt) {
+    ASSERT_EQ(excpt.GetOrtErrorCode(), ORT_INVALID_ARGUMENT);
+    ASSERT_THAT(excpt.what(), testing::HasSubstr("context_file_path should not point to a folder."));
+  }
+}
+
+// Create session 1 to generate context binary file
+// Create session 2 to do same thing, make sure session 2 failed because file exist already
+// Make sure no new file over write from session 2
+TEST_F(QnnHTPBackendTests, QnnContextBinaryGenerationNoOverWrite) {
+  ProviderOptions provider_options;
+#if defined(_WIN32)
+  provider_options["backend_path"] = "QnnHtp.dll";
+#else
+  provider_options["backend_path"] = "libQnnHtp.so";
+#endif
+  provider_options["offload_graph_io_quantization"] = "0";
+
+  const std::unordered_map<std::string, int> domain_to_version = {{"", 13}, {kMSDomain, 1}};
+
+  auto& logging_manager = DefaultLoggingManager();
+  logging_manager.SetDefaultLoggerSeverity(logging::Severity::kERROR);
+
+  onnxruntime::Model model("QNN_EP_TestModel", false, ModelMetaData(), PathString(),
+                           IOnnxRuntimeOpSchemaRegistryList(), domain_to_version, {},
+                           logging_manager.DefaultLogger());
+  Graph& graph = model.MainGraph();
+  ModelTestBuilder helper(graph);
+  bool single_ep_node = true;
+  BuildGraphWithQAndNonQ(single_ep_node)(helper);
+  helper.SetGraphOutputs();
+  ASSERT_STATUS_OK(model.MainGraph().Resolve());
+
+  // Serialize the model to a string.
+  std::string model_data;
+  model.ToProto().SerializeToString(&model_data);
+
+  const auto model_data_span = AsByteSpan(model_data.data(), model_data.size());
+
+  const std::string ep_context_onnx_file = "./ep_context_no_over_write.onnx";
+  const std::string ep_context_binary_file = "./ep_context_no_over_write.onnx_QNNExecutionProvider_QNN_10880527342279992768_1_0.bin";
+
+  std::remove(ep_context_onnx_file.c_str());
+  Ort::SessionOptions so;
+  so.AddConfigEntry(kOrtSessionOptionEpContextEnable, "1");
+  so.AddConfigEntry(kOrtSessionOptionEpContextFilePath, ep_context_onnx_file.c_str());
+  so.AppendExecutionProvider("QNN", provider_options);
+
+  Ort::Session session1(*ort_env, model_data_span.data(), model_data_span.size(), so);
+
+  auto modify_time_1 = std::filesystem::last_write_time(ep_context_binary_file);
+
+  try {
+    Ort::Session session2(*ort_env, model_data_span.data(), model_data_span.size(), so);
+    FAIL();  // Should not get here!
+  } catch (const Ort::Exception& excpt) {
+    ASSERT_EQ(excpt.GetOrtErrorCode(), ORT_FAIL);
+    ASSERT_THAT(excpt.what(), testing::HasSubstr("exist already."));
+    auto modify_time_2 = std::filesystem::last_write_time(ep_context_binary_file);
+    ASSERT_EQ(modify_time_1, modify_time_2);
+  }
+
+  ASSERT_EQ(std::remove(ep_context_onnx_file.c_str()), 0);
+  ASSERT_EQ(std::remove(ep_context_binary_file.c_str()), 0);
+}
+
 // Create a model with Case + Add (quantized)
 // cast_input -> Cast -> Q -> DQ \
 //                                Add -> Q -> DQ -> output