diff --git a/.github/workflows/windows_qnn_x64.yml b/.github/workflows/windows_qnn_x64.yml
index 9788792b94fa8..6e8431c0ee991 100644
--- a/.github/workflows/windows_qnn_x64.yml
+++ b/.github/workflows/windows_qnn_x64.yml
@@ -47,14 +47,14 @@ jobs:
       - 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 .
+          azcopy.exe cp --recursive https://lotusscus.blob.core.windows.net/models/qnnsdk/qnn-v2.39.0.250926 .
           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"
+          $qnn_sdk_path = Join-Path $env:RUNNER_TEMP "qnn-v2.39.0.250926"
           echo "QNN_SDK_ROOT=$qnn_sdk_path" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
           echo "QNN SDK Root: $qnn_sdk_path"
           dir $qnn_sdk_path
diff --git a/tools/ci_build/github/azure-pipelines/android-arm64-v8a-QNN-crosscompile-ci-pipeline.yml b/tools/ci_build/github/azure-pipelines/android-arm64-v8a-QNN-crosscompile-ci-pipeline.yml
index 61715de88c14e..de7beb7c5c092 100644
--- a/tools/ci_build/github/azure-pipelines/android-arm64-v8a-QNN-crosscompile-ci-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/android-arm64-v8a-QNN-crosscompile-ci-pipeline.yml
@@ -32,7 +32,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 jobs:
 - job: Build_QNN_EP
diff --git a/tools/ci_build/github/azure-pipelines/c-api-noopenmp-packaging-pipelines.yml b/tools/ci_build/github/azure-pipelines/c-api-noopenmp-packaging-pipelines.yml
index 91736752e22d4..604b299b86736 100644
--- a/tools/ci_build/github/azure-pipelines/c-api-noopenmp-packaging-pipelines.yml
+++ b/tools/ci_build/github/azure-pipelines/c-api-noopenmp-packaging-pipelines.yml
@@ -55,7 +55,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 resources:
   repositories:
diff --git a/tools/ci_build/github/azure-pipelines/c-api-noopenmp-test-pipelines.yml b/tools/ci_build/github/azure-pipelines/c-api-noopenmp-test-pipelines.yml
index 46363c07b3e3e..ca522086ae862 100644
--- a/tools/ci_build/github/azure-pipelines/c-api-noopenmp-test-pipelines.yml
+++ b/tools/ci_build/github/azure-pipelines/c-api-noopenmp-test-pipelines.yml
@@ -83,7 +83,7 @@ stages:
       artifactName: 'onnxruntime-android-qnn-aar'
       packageName: 'onnxruntime-android-qnn'
       #TODO: get this information from the setup stage
-      QnnSDKVersion: '2.38.0.250901'
+      QnnSDKVersion: '2.39.0.250926'
 
 - template: nuget/templates/test_win.yml
   parameters:
@@ -266,4 +266,4 @@ stages:
           inputs:
             scriptPath: '$(Build.SourcesDirectory)\tools\ci_build\build.py'
             arguments: '--config RelWithDebInfo --use_binskim_compliant_compile_flags --enable_lto --disable_rtti --build_dir $(Build.BinariesDirectory) --skip_submodule_sync --build_shared_lib --test --enable_onnx_tests'
-            workingDirectory: '$(Build.BinariesDirectory)'
\ No newline at end of file
+            workingDirectory: '$(Build.BinariesDirectory)'
diff --git a/tools/ci_build/github/azure-pipelines/custom-nuget-packaging-pipeline.yml b/tools/ci_build/github/azure-pipelines/custom-nuget-packaging-pipeline.yml
index 1ad6f411d9848..851b75f9e4a65 100644
--- a/tools/ci_build/github/azure-pipelines/custom-nuget-packaging-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/custom-nuget-packaging-pipeline.yml
@@ -6,7 +6,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 - name: IsReleaseBuild
   displayName: Is a release build? Set it to true if you are doing an Onnx Runtime release.
diff --git a/tools/ci_build/github/azure-pipelines/linux-qnn-ci-pipeline.yml b/tools/ci_build/github/azure-pipelines/linux-qnn-ci-pipeline.yml
index a9e0780cb4f17..6e6977bb76f12 100644
--- a/tools/ci_build/github/azure-pipelines/linux-qnn-ci-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/linux-qnn-ci-pipeline.yml
@@ -33,7 +33,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 jobs:
   - job: Build_QNN_EP
diff --git a/tools/ci_build/github/azure-pipelines/py-packaging-pipeline.yml b/tools/ci_build/github/azure-pipelines/py-packaging-pipeline.yml
index 1f716b1c46d61..12dbda7503973 100644
--- a/tools/ci_build/github/azure-pipelines/py-packaging-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/py-packaging-pipeline.yml
@@ -59,7 +59,7 @@ parameters:
 - name: qnn_sdk_version
   type: string
   displayName: 'QNN SDK version. Only for QNN packages.'
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 trigger: none
 
diff --git a/tools/ci_build/github/azure-pipelines/qnn-ep-nuget-packaging-pipeline.yml b/tools/ci_build/github/azure-pipelines/qnn-ep-nuget-packaging-pipeline.yml
index 250337f056d89..53a803f957420 100644
--- a/tools/ci_build/github/azure-pipelines/qnn-ep-nuget-packaging-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/qnn-ep-nuget-packaging-pipeline.yml
@@ -2,7 +2,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 - name: build_config
   displayName: Build Configuration
diff --git a/tools/ci_build/github/azure-pipelines/stages/py-cpu-packaging-stage.yml b/tools/ci_build/github/azure-pipelines/stages/py-cpu-packaging-stage.yml
index 43e3a0132444e..28512fd8686db 100644
--- a/tools/ci_build/github/azure-pipelines/stages/py-cpu-packaging-stage.yml
+++ b/tools/ci_build/github/azure-pipelines/stages/py-cpu-packaging-stage.yml
@@ -59,7 +59,7 @@ parameters:
 - name: qnn_sdk_version
   type: string
   displayName: 'QNN SDK version. Only for QNN packages.'
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 stages:
 - ${{ if eq(parameters.enable_windows_cpu, true) }}:
diff --git a/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar-test.yml b/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar-test.yml
index c4e935aa60b48..42b607eabcc40 100644
--- a/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar-test.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar-test.yml
@@ -19,7 +19,7 @@ parameters:
 - name: QnnSDKVersion
   displayName: QNN SDK Version
   type: string
-  default: '2.38.0.250901'
+  default: '2.39.0.250926'
 
 - name: enableWebGpu
   displayName: Enable WebGPU test
diff --git a/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar.yml b/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar.yml
index 73c84cf50e785..38de9e1ad8fbc 100644
--- a/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/android-java-api-aar.yml
@@ -53,7 +53,7 @@ parameters:
 - name: QnnSDKVersion
   displayName: QNN SDK Version
   type: string
-  default: '2.38.0.250901'
+  default: '2.39.0.250926'
 
 - name: is1ES
   displayName: Is 1ES pipeline
@@ -148,4 +148,4 @@ jobs:
 
   - template: jar-maven-signing-linux.yml
     parameters:
-      JarFileDirectory: $(Build.BinariesDirectory)/.artifacts
\ No newline at end of file
+      JarFileDirectory: $(Build.BinariesDirectory)/.artifacts
diff --git a/tools/ci_build/github/azure-pipelines/templates/c-api-cpu.yml b/tools/ci_build/github/azure-pipelines/templates/c-api-cpu.yml
index 2a6f8461d773c..6d29101dc17ad 100644
--- a/tools/ci_build/github/azure-pipelines/templates/c-api-cpu.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/c-api-cpu.yml
@@ -46,7 +46,7 @@ parameters:
 - name: QnnSDKVersion
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 - name: is1ES
   displayName: Is 1ES pipeline
diff --git a/tools/ci_build/github/azure-pipelines/templates/jobs/download_linux_qnn_sdk.yml b/tools/ci_build/github/azure-pipelines/templates/jobs/download_linux_qnn_sdk.yml
index 4bf4b673c5d27..8442d6db4feb4 100644
--- a/tools/ci_build/github/azure-pipelines/templates/jobs/download_linux_qnn_sdk.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/jobs/download_linux_qnn_sdk.yml
@@ -1,7 +1,7 @@
 parameters:
   - name: QnnSDKVersion
     type: string
-    default: '2.38.0.250901'
+    default: '2.39.0.250926'
 
 steps:
   - script: |
diff --git a/tools/ci_build/github/azure-pipelines/templates/jobs/download_win_qnn_sdk.yml b/tools/ci_build/github/azure-pipelines/templates/jobs/download_win_qnn_sdk.yml
index 6a01b7f6f4d19..61e67910f5c9c 100644
--- a/tools/ci_build/github/azure-pipelines/templates/jobs/download_win_qnn_sdk.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/jobs/download_win_qnn_sdk.yml
@@ -1,7 +1,7 @@
 parameters:
   - name: QnnSDKVersion
     type: string
-    default: '2.38.0.250901'
+    default: '2.39.0.250926'
 
 steps:
   - powershell: |
diff --git a/tools/ci_build/github/azure-pipelines/templates/jobs/init_linux_qnn_sdk_x64.yml b/tools/ci_build/github/azure-pipelines/templates/jobs/init_linux_qnn_sdk_x64.yml
index dae1c739acb25..b1dd26ff8da93 100644
--- a/tools/ci_build/github/azure-pipelines/templates/jobs/init_linux_qnn_sdk_x64.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/jobs/init_linux_qnn_sdk_x64.yml
@@ -1,7 +1,7 @@
 parameters:
   - name: QnnSDKVersion
     type: string
-    default: '2.38.0.250901'
+    default: '2.39.0.250926'
 
 steps:
   - bash: |
diff --git a/tools/ci_build/github/azure-pipelines/templates/py-linux-qnn.yml b/tools/ci_build/github/azure-pipelines/templates/py-linux-qnn.yml
index b9e9d5e308080..cd3b93ac9d18a 100644
--- a/tools/ci_build/github/azure-pipelines/templates/py-linux-qnn.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/py-linux-qnn.yml
@@ -26,7 +26,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
   
 - name: is1ES
   displayName: 'Whether the pipeline is running in 1ES'
diff --git a/tools/ci_build/github/azure-pipelines/templates/py-win-arm64-qnn.yml b/tools/ci_build/github/azure-pipelines/templates/py-win-arm64-qnn.yml
index 64ffffeac2bcd..2ee7ebc9560ac 100644
--- a/tools/ci_build/github/azure-pipelines/templates/py-win-arm64-qnn.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/py-win-arm64-qnn.yml
@@ -11,7 +11,7 @@ parameters:
 - name: QNN_SDK
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 - name: ENV_SETUP_SCRIPT
   type: string
diff --git a/tools/ci_build/github/azure-pipelines/templates/py-win-arm64ec-qnn.yml b/tools/ci_build/github/azure-pipelines/templates/py-win-arm64ec-qnn.yml
index 1f3315840e92c..c5c88a6aee9d5 100644
--- a/tools/ci_build/github/azure-pipelines/templates/py-win-arm64ec-qnn.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/py-win-arm64ec-qnn.yml
@@ -7,7 +7,7 @@ parameters:
 - name: QNN_SDK
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 - name: ENV_SETUP_SCRIPT
   type: string
diff --git a/tools/ci_build/github/azure-pipelines/templates/py-win-x64-qnn.yml b/tools/ci_build/github/azure-pipelines/templates/py-win-x64-qnn.yml
index 5a0707081d642..6cc1de0852db4 100644
--- a/tools/ci_build/github/azure-pipelines/templates/py-win-x64-qnn.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/py-win-x64-qnn.yml
@@ -7,7 +7,7 @@ parameters:
 - name: QNN_SDK
   displayName: QNN SDK Version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 - name: ENV_SETUP_SCRIPT
   type: string
diff --git a/tools/ci_build/github/azure-pipelines/templates/qnn-ep-win.yml b/tools/ci_build/github/azure-pipelines/templates/qnn-ep-win.yml
index 2221c93ecc5d0..90cd6ccf6d110 100644
--- a/tools/ci_build/github/azure-pipelines/templates/qnn-ep-win.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/qnn-ep-win.yml
@@ -1,5 +1,5 @@
 parameters:
-  QnnSdk: '2.38.0.250901'
+  QnnSdk: '2.39.0.250926'
   build_config: 'RelWithDebInfo'
   IsReleaseBuild: false
   DoEsrp: false
diff --git a/tools/ci_build/github/azure-pipelines/win-qnn-arm64-ci-pipeline.yml b/tools/ci_build/github/azure-pipelines/win-qnn-arm64-ci-pipeline.yml
index ba753f0b3b657..c0a9c235fd542 100644
--- a/tools/ci_build/github/azure-pipelines/win-qnn-arm64-ci-pipeline.yml
+++ b/tools/ci_build/github/azure-pipelines/win-qnn-arm64-ci-pipeline.yml
@@ -33,7 +33,7 @@ parameters:
 - name: QnnSdk
   displayName: QNN SDK version
   type: string
-  default: 2.38.0.250901
+  default: 2.39.0.250926
 
 jobs:
 - job: 'BUILD_QNN_EP'