diff --git a/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc b/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc
index 6e09f494f4a8d..bca41b7851c28 100644
--- a/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc
+++ b/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc
@@ -18,8 +18,11 @@
 #include "core/framework/data_transfer_manager.h"
 #include "core/framework/fallback_cpu_capability.h"
 #include "core/framework/kernel_registry.h"
+#include "core/framework/run_options.h"
 #include "core/graph/function_utils.h"
 #include "core/graph/indexed_sub_graph.h"
+#include "core/session/onnxruntime_run_options_config_keys.h"
+#include "core/common/parse_string.h"
 
 #include "core/providers/webgpu/webgpu_context.h"
 #include "core/providers/webgpu/data_transfer.h"
@@ -692,7 +695,6 @@ std::unique_ptr<KernelRegistry> RegisterKernels() {
       BuildKernelCreateInfo<ONNX_OPERATOR_VERSIONED_KERNEL_CLASS_NAME(kWebGpuExecutionProvider, kOnnxDomain, 11, 12, Flatten)>,
       BuildKernelCreateInfo<ONNX_OPERATOR_VERSIONED_KERNEL_CLASS_NAME(kWebGpuExecutionProvider, kOnnxDomain, 13, 20, Flatten)>,
       BuildKernelCreateInfo<ONNX_OPERATOR_KERNEL_CLASS_NAME(kWebGpuExecutionProvider, kOnnxDomain, 21, Flatten)>,
-
       BuildKernelCreateInfo<ONNX_OPERATOR_VERSIONED_KERNEL_CLASS_NAME(kWebGpuExecutionProvider, kOnnxDomain, 6, 12, Tile)>,
       BuildKernelCreateInfo<ONNX_OPERATOR_KERNEL_CLASS_NAME(kWebGpuExecutionProvider, kOnnxDomain, 13, Tile)>,
 
@@ -907,7 +909,7 @@ Status WebGpuExecutionProvider::OnSessionInitializationEnd() {
   return Status::OK();
 }
 
-Status WebGpuExecutionProvider::OnRunStart(const onnxruntime::RunOptions& /*run_options*/) {
+Status WebGpuExecutionProvider::OnRunStart(const onnxruntime::RunOptions& run_options) {
   if (context_.ValidationMode() >= ValidationMode::Basic) {
     context_.PushErrorScope();
   }
@@ -916,20 +918,32 @@ Status WebGpuExecutionProvider::OnRunStart(const onnxruntime::RunOptions& /*run_
     context_.StartProfiling();
   }
 
-  if (IsGraphCaptureEnabled() && IsGraphCaptureAllowed() && !IsGraphCaptured(0)) {
-    context_.CaptureBegin(&captured_commands_, *graph_buffer_mgr_);
+  if (IsGraphCaptureEnabled()) {
+    auto graph_annotation_str = run_options.config_options.GetConfigEntry(kOrtRunOptionsConfigCudaGraphAnnotation);
+    int graph_annotation_id = 0;
+    if (graph_annotation_str.has_value()) {
+      ORT_ENFORCE(onnxruntime::TryParseStringWithClassicLocale<int>(*graph_annotation_str, graph_annotation_id),
+                  "Failed to parse the graph annotation id: ",
+                  *graph_annotation_str);
+    }
+
+    if (graph_annotation_id != -1 && IsGraphCaptureAllowed() && !IsGraphCaptured(graph_annotation_id)) {
+      context_.CaptureBegin(&captured_commands_, *graph_buffer_mgr_);
+    }
+    m_current_graph_annotation_id = graph_annotation_id;
   }
 
   return Status::OK();
 }
 
-Status WebGpuExecutionProvider::OnRunEnd(bool /* sync_stream */, const onnxruntime::RunOptions& /*run_options*/) {
+Status WebGpuExecutionProvider::OnRunEnd(bool /* sync_stream */, const onnxruntime::RunOptions& /* run_options */) {
   context_.Flush(BufferManager());
 
-  if (IsGraphCaptureEnabled() && !IsGraphCaptured(0)) {
-    if (IsGraphCaptureAllowed()) {
+  if (IsGraphCaptureEnabled() && !IsGraphCaptured(m_current_graph_annotation_id)) {
+    if (m_current_graph_annotation_id != -1 && IsGraphCaptureAllowed()) {
       context_.CaptureEnd();
       is_graph_captured_ = true;
+      ORT_RETURN_IF_ERROR(ReplayGraph(m_current_graph_annotation_id));
     } else {
       IncrementRegularRunCountBeforeGraphCapture();
     }
@@ -952,12 +966,12 @@ bool WebGpuExecutionProvider::IsGraphCaptureEnabled() const {
   return enable_graph_capture_;
 }
 
-bool WebGpuExecutionProvider::IsGraphCaptured(int) const {
-  return is_graph_captured_;
+bool WebGpuExecutionProvider::IsGraphCaptured(int graph_annotation_id) const {
+  return is_graph_captured_ && graph_annotation_id != -1;
 }
 
-Status WebGpuExecutionProvider::ReplayGraph(int) {
-  ORT_ENFORCE(IsGraphCaptured(0));
+Status WebGpuExecutionProvider::ReplayGraph(int graph_annotation_id) {
+  ORT_ENFORCE(IsGraphCaptured(graph_annotation_id));
   context_.Replay(captured_commands_, *graph_buffer_mgr_);
   return Status::OK();
 }
diff --git a/onnxruntime/core/providers/webgpu/webgpu_execution_provider.h b/onnxruntime/core/providers/webgpu/webgpu_execution_provider.h
index 2567be2a1eb18..3bbec164a0190 100644
--- a/onnxruntime/core/providers/webgpu/webgpu_execution_provider.h
+++ b/onnxruntime/core/providers/webgpu/webgpu_execution_provider.h
@@ -99,6 +99,7 @@ class WebGpuExecutionProvider : public IExecutionProvider {
   bool is_graph_captured_ = false;
   int regular_run_count_before_graph_capture_ = 0;
   const int min_num_runs_before_cuda_graph_capture_ = 1;  // required min regular runs before graph capture for the necessary memory allocations.
+  int m_current_graph_annotation_id = 0;
   webgpu::GpuBufferAllocator* allocator_ = nullptr;
 
   // Buffer manager specifically for graph capture mode