diff --git a/.changeset/remove-app-scaffold-extension-command.md b/.changeset/remove-app-scaffold-extension-command.md
new file mode 100644
index 00000000000..6c20a9332f3
--- /dev/null
+++ b/.changeset/remove-app-scaffold-extension-command.md
@@ -0,0 +1,5 @@
+---
+'@shopify/app': major
+---
+
+Remove the deprecated `shopify app scaffold extension` command. Use `shopify app generate extension` instead. (The command was already unregistered from the CLI command map but the file remained on disk; this change deletes the orphaned source file.)
diff --git a/packages/app/src/cli/commands/app/scaffold/extension.ts b/packages/app/src/cli/commands/app/scaffold/extension.ts
deleted file mode 100644
index fa2c7f1cf5a..00000000000
--- a/packages/app/src/cli/commands/app/scaffold/extension.ts
+++ /dev/null
@@ -1,25 +0,0 @@
-import {AppLinkedCommandOutput} from '../../../utilities/app-linked-command.js'
-import AppGenerateExtension from '../generate/extension.js'
-import {renderWarning} from '@shopify/cli-kit/node/ui'
-
-class AppScaffoldExtension extends AppGenerateExtension {
-  static description = 'Scaffold an Extension.'
-  static hidden = true
-  public async run(): Promise<AppLinkedCommandOutput> {
-    renderWarning({
-      headline: [
-        'The command',
-        {command: 'scaffold'},
-        'has been deprecated in favor of',
-        {command: 'generate'},
-        'and will be eventually deleted.',
-        'You might need to update the',
-        {command: 'scaffold'},
-        "script in the project's package.json.",
-      ],
-    })
-    return super.run()
-  }
-}
-
-export default AppScaffoldExtension