diff --git a/common/changes/@microsoft/rush/fix-rush-pnpm-npm-config-warnings_2026-03-23-18-16.json b/common/changes/@microsoft/rush/fix-rush-pnpm-npm-config-warnings_2026-03-23-18-16.json
new file mode 100644
index 0000000000..219d8b2423
--- /dev/null
+++ b/common/changes/@microsoft/rush/fix-rush-pnpm-npm-config-warnings_2026-03-23-18-16.json
@@ -0,0 +1,10 @@
+{
+  "changes": [
+    {
+      "packageName": "@microsoft/rush",
+      "comment": "Fix \"Unknown env config\" warnings from npm during rush-pnpm operations (e.g. publish) by passing pnpm configuration via CLI args instead of NPM_CONFIG_* environment variables.",
+      "type": "none"
+    }
+  ],
+  "packageName": "@microsoft/rush"
+}
diff --git a/libraries/rush-lib/src/cli/RushPnpmCommandLineParser.ts b/libraries/rush-lib/src/cli/RushPnpmCommandLineParser.ts
index 1980c57f08..3a04deb7a7 100644
--- a/libraries/rush-lib/src/cli/RushPnpmCommandLineParser.ts
+++ b/libraries/rush-lib/src/cli/RushPnpmCommandLineParser.ts
@@ -432,12 +432,16 @@ export class RushPnpmCommandLineParser {
     const rushConfiguration: RushConfiguration = this._rushConfiguration;
     const workspaceFolder: string = this._subspace.getSubspaceTempFolderPath();
     const pnpmEnvironmentMap: EnvironmentMap = new EnvironmentMap(process.env);
-    pnpmEnvironmentMap.set('NPM_CONFIG_WORKSPACE_DIR', workspaceFolder);
+
+    // Pass pnpm configuration as CLI args rather than NPM_CONFIG_* environment variables.
+    // Using env vars like NPM_CONFIG_STORE_DIR would cause "Unknown env config" warnings
+    // when pnpm internally delegates to npm (e.g. during publish operations).
+    const pnpmConfigArgs: string[] = [`--config.workspaceDir=${workspaceFolder}`];
 
     if (rushConfiguration.pnpmOptions.pnpmStorePath) {
-      pnpmEnvironmentMap.set('NPM_CONFIG_STORE_DIR', rushConfiguration.pnpmOptions.pnpmStorePath);
-      pnpmEnvironmentMap.set('NPM_CONFIG_CACHE_DIR', rushConfiguration.pnpmOptions.pnpmStorePath);
-      pnpmEnvironmentMap.set('NPM_CONFIG_STATE_DIR', rushConfiguration.pnpmOptions.pnpmStorePath);
+      pnpmConfigArgs.push(`--store-dir=${rushConfiguration.pnpmOptions.pnpmStorePath}`);
+      pnpmConfigArgs.push(`--config.cacheDir=${rushConfiguration.pnpmOptions.pnpmStorePath}`);
+      pnpmConfigArgs.push(`--config.stateDir=${rushConfiguration.pnpmOptions.pnpmStorePath}`);
     }
 
     if (rushConfiguration.pnpmOptions.environmentVariables) {
@@ -473,7 +477,7 @@ export class RushPnpmCommandLineParser {
     try {
       const { exitCode } = await Utilities.executeCommandAsync({
         command: rushConfiguration.packageManagerToolFilename,
-        args: this._pnpmArgs,
+        args: [...pnpmConfigArgs, ...this._pnpmArgs],
         workingDirectory: process.cwd(),
         environment: pnpmEnvironmentMap.toObject(),
         keepEnvironment: true,