diff --git a/common/changes/@microsoft/rush/fix-pnpm-sync-modules-yaml_2025-06-23-08-37.json b/common/changes/@microsoft/rush/fix-pnpm-sync-modules-yaml_2025-06-23-08-37.json
new file mode 100644
index 00000000000..9bf79c201b2
--- /dev/null
+++ b/common/changes/@microsoft/rush/fix-pnpm-sync-modules-yaml_2025-06-23-08-37.json
@@ -0,0 +1,10 @@
+{
+  "changes": [
+    {
+      "packageName": "@microsoft/rush",
+      "comment": "Fix pnpm-sync caused .modules.yaml ENOENT during install",
+      "type": "none"
+    }
+  ],
+  "packageName": "@microsoft/rush"
+}
\ No newline at end of file
diff --git a/libraries/rush-lib/src/logic/base/BaseInstallManager.ts b/libraries/rush-lib/src/logic/base/BaseInstallManager.ts
index 2bb9ec8afcf..f6c15e0e3e1 100644
--- a/libraries/rush-lib/src/logic/base/BaseInstallManager.ts
+++ b/libraries/rush-lib/src/logic/base/BaseInstallManager.ts
@@ -293,11 +293,12 @@ export abstract class BaseInstallManager {
     if (this.rushConfiguration.isPnpm && experiments?.usePnpmSyncForInjectedDependencies) {
       const pnpmLockfilePath: string = subspace.getTempShrinkwrapFilename();
       const dotPnpmFolder: string = `${subspace.getSubspaceTempFolderPath()}/node_modules/.pnpm`;
+      const modulesFilePath: string = `${subspace.getSubspaceTempFolderPath()}/node_modules/.modules.yaml`;
 
       // we have an edge case here
       // if a package.json has no dependencies, pnpm will still generate the pnpm-lock.yaml but not .pnpm folder
       // so we need to make sure pnpm-lock.yaml and .pnpm exists before calling the pnpmSync APIs
-      if ((await FileSystem.existsAsync(pnpmLockfilePath)) && (await FileSystem.existsAsync(dotPnpmFolder))) {
+      if ((await FileSystem.existsAsync(pnpmLockfilePath)) && (await FileSystem.existsAsync(dotPnpmFolder)) && (await FileSystem.existsAsync(modulesFilePath))) {
         await pnpmSyncPrepareAsync({
           lockfilePath: pnpmLockfilePath,
           dotPnpmFolder,