diff --git a/.github/workflows/windows_qnn_x64.yml b/.github/workflows/windows_qnn_x64.yml
new file mode 100644
index 0000000000000..549af2b63b97e
--- /dev/null
+++ b/.github/workflows/windows_qnn_x64.yml
@@ -0,0 +1,82 @@
+name: Windows x64 QNN CI Pipeline
+
+on:
+  push:
+    branches:
+      - main
+      - rel-*
+  pull_request:
+    branches:
+      - main
+      - rel-*
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.ref || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  build_test_qnn_ep:
+    name: Windows x64 QNN CI Pipeline (${{ matrix.QnnLibKind }})
+    runs-on: ["self-hosted", "1ES.Pool=onnxruntime-github-vs2022-mms"]
+    timeout-minutes: 120
+    strategy:
+      matrix: 
+        QnnLibKind: [shared_lib, static_lib]
+    env:
+      AZCOPY_AUTO_LOGIN_TYPE: MSI
+      AZCOPY_MSI_CLIENT_ID: 63b63039-6328-442f-954b-5a64d124e5b4
+      DOTNET_SKIP_FIRST_TIME_EXPERIENCE: true
+      ALLOW_RELEASED_ONNX_OPSET_ONLY: '1'
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          architecture: x64
+
+      - name: Locate vcvarsall and Setup Env
+        uses: ./.github/actions/locate-vcvarsall-and-setup-env
+        with:
+          architecture: x64
+
+      - name: Download QNN SDK
+        working-directory: ${{ runner.temp }}
+        run: |
+          azcopy.exe cp --recursive https://lotusscus.blob.core.windows.net/models/qnnsdk/qnn-v2.38.0.250901 .
+          dir
+        shell: pwsh
+            
+      - name: Set QNN_SDK_ROOT environment variable
+        shell: pwsh
+        run: |
+          $qnn_sdk_path = Join-Path $env:RUNNER_TEMP "qnn-v2.38.0.250901"
+          echo "QNN_SDK_ROOT=$qnn_sdk_path" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+          echo "QNN SDK Root: $qnn_sdk_path"
+          dir $qnn_sdk_path
+
+      - name: Build and Test
+        shell: cmd
+        run: |
+          python ${{ github.workspace }}\tools\ci_build\build.py --config RelWithDebInfo --build_dir ${{ runner.temp }}\build --cmake_generator "Visual Studio 17 2022" --build_java --build_shared_lib --use_qnn ${{ matrix.QnnLibKind }} --qnn_home %QNN_SDK_ROOT% --use_binskim_compliant_compile_flags --update --build --test --enable_onnx_tests --parallel
+
+      - name: Run ONNX Tests
+        shell: cmd
+        working-directory: ${{ runner.temp }}\build\RelWithDebInfo\RelWithDebInfo
+        run: |
+          .\onnx_test_runner -j 1 -e qnn -i "backend_path|%QNN_SDK_ROOT%\lib\x86_64-windows-msvc\QnnCpu.dll" ${{ github.workspace }}\cmake\external\onnx\onnx\backend\test\data\node
+
+      - name: Run float32 model tests
+        shell: cmd
+        working-directory: ${{ runner.temp }}\build\RelWithDebInfo\RelWithDebInfo
+        run: |
+          rem This step assumes the model data exists at C:\data\float32_models on the runner
+          if exist C:\data\float32_models (
+            .\onnx_test_runner -j 1 -e qnn -i "backend_path|%QNN_SDK_ROOT%\lib\x86_64-windows-msvc\QnnCpu.dll" C:\data\float32_models
+          ) else (
+            echo "Skipping float32 model tests: C:\data\float32_models not found."
+          )
diff --git a/tools/ci_build/github/azure-pipelines/win-qnn-ci-pipeline.yml b/tools/ci_build/github/azure-pipelines/win-qnn-ci-pipeline.yml
deleted file mode 100644
index 48e6b9c986351..0000000000000
--- a/tools/ci_build/github/azure-pipelines/win-qnn-ci-pipeline.yml
+++ /dev/null
@@ -1,112 +0,0 @@
-##### start trigger Don't edit it manually, Please do edit set-trigger-rules.py ####
-### please do rerun set-trigger-rules.py ###
-trigger:
-  branches:
-    include:
-    - main
-    - rel-*
-  paths:
-    exclude:
-    - docs/**
-    - README.md
-    - CONTRIBUTING.md
-    - BUILD.md
-    - 'js/web'
-    - 'onnxruntime/core/providers/js'
-pr:
-  branches:
-    include:
-    - main
-    - rel-*
-  paths:
-    exclude:
-    - docs/**
-    - README.md
-    - CONTRIBUTING.md
-    - BUILD.md
-    - 'js/web'
-    - 'onnxruntime/core/providers/js'
-#### end trigger ####
-
-parameters:
-
-- name: QnnSdk
-  displayName: QNN SDK version
-  type: string
-  default: 2.38.0.250901
-
-jobs:
-- job: 'BUILD_QNN_EP'
-  pool: 'Onnxruntime-QNNEP-Windows-2022-CPU'
-  variables:
-    MsbuildArguments: '-detailedsummary -maxcpucount -consoleloggerparameters:PerformanceSummary'
-    OnnxRuntimeBuildDirectory: '$(Build.BinariesDirectory)'
-    DOTNET_SKIP_FIRST_TIME_EXPERIENCE: true
-    buildArch: x64
-    setVcvars: true
-    BuildConfig: 'RelWithDebInfo'
-    ALLOW_RELEASED_ONNX_OPSET_ONLY: '1'
-    TODAY: $[format('{0:dd}{0:MM}{0:yyyy}', pipeline.startTime)]
-  timeoutInMinutes: 120
-  workspace:
-    clean: all
-  strategy:
-    matrix:
-      SHARED_LIB:
-        QnnLibKind: 'shared_lib'
-      STATIC_LIB:
-        QnnLibKind: 'static_lib'
-  steps:
-
-  - task: UsePythonVersion@0
-    inputs:
-      versionSpec: '3.12'
-      addToPath: true
-      architecture: $(buildArch)
-
-  - template: templates/jobs/download_win_qnn_sdk.yml
-    parameters:
-      QnnSDKVersion: ${{ parameters.QnnSdk }}
-
-  - template: templates/jobs/win-ci-build-steps.yml
-    parameters:
-      WithCache: True
-      Today: $(TODAY)
-      AdditionalKey: "win-qnn | $(BuildConfig)"
-      BuildPyArguments: >-
-        --config $(BuildConfig)
-        --build_dir $(Build.BinariesDirectory)
-        --cmake_generator "Visual Studio 17 2022"
-        --build_java
-        --build_shared_lib
-        --use_qnn $(QnnLibKind)
-        --qnn_home $(QnnSDKRootDir)
-        --use_binskim_compliant_compile_flags
-        --update --parallel
-      MsbuildArguments: $(MsbuildArguments)
-      BuildArch: $(buildArch)
-      Platform: 'x64'
-      BuildConfig: $(BuildConfig)
-
-  - script: |
-      python $(Build.SourcesDirectory)\tools\ci_build\build.py ^
-        --config $(BuildConfig) ^
-        --build_dir $(Build.BinariesDirectory) ^
-        --cmake_generator "Visual Studio 17 2022" ^
-        --build_java ^
-        --build_shared_lib ^
-        --use_qnn $(QnnLibKind) ^
-        --qnn_home $(QnnSDKRootDir) ^
-        --use_binskim_compliant_compile_flags ^
-        --test --enable_onnx_tests
-    displayName: 'Run unit tests'
-
-  - script: |
-      .\$(BuildConfig)\onnx_test_runner -j 1 -e qnn -i "backend_path|$(QnnSDKRootDir)\lib\x86_64-windows-msvc\QnnCpu.dll" $(Build.SourcesDirectory)\cmake\external\onnx\onnx\backend\test\data\node
-    workingDirectory: '$(Build.BinariesDirectory)\$(BuildConfig)'
-    displayName: 'Run ONNX Tests'
-
-  - script: |
-      .\$(BuildConfig)\onnx_test_runner -j 1 -e qnn -i "backend_path|$(QnnSDKRootDir)\lib\x86_64-windows-msvc\QnnCpu.dll" C:\data\float32_models
-    workingDirectory: '$(Build.BinariesDirectory)\$(BuildConfig)'
-    displayName: 'Run float32 model tests'