diff --git a/pkg/workflow/checkout_step_generator.go b/pkg/workflow/checkout_step_generator.go
index 6216c8cbc99..993593f17c6 100644
--- a/pkg/workflow/checkout_step_generator.go
+++ b/pkg/workflow/checkout_step_generator.go
@@ -25,6 +25,10 @@ func (cm *CheckoutManager) GenerateCheckoutAppTokenSteps(c *Compiler, permission
 		stepID := fmt.Sprintf("checkout-app-token-%d", i)
 		for _, step := range appSteps {
 			modified := strings.ReplaceAll(step, "id: safe-outputs-app-token", "id: "+stepID)
+			// Rename the step to make it unique when multiple checkouts use app auth.
+			// This prevents duplicate step name errors when more than one checkout entry
+			// falls back to the top-level github-app (or has its own github-app configured).
+			modified = strings.ReplaceAll(modified, "name: Generate GitHub App token", fmt.Sprintf("name: Generate GitHub App token for checkout (%d)", i))
 			steps = append(steps, modified)
 		}
 	}
diff --git a/pkg/workflow/duplicate_step_validation_integration_test.go b/pkg/workflow/duplicate_step_validation_integration_test.go
index 92283543ff3..d8a4ceed56f 100644
--- a/pkg/workflow/duplicate_step_validation_integration_test.go
+++ b/pkg/workflow/duplicate_step_validation_integration_test.go
@@ -89,3 +89,97 @@ This workflow tests that duplicate checkout steps are properly deduplicated.
 
 	t.Logf("✓ Duplicate step validation working correctly: found %d checkout step(s) in safe_outputs job (deduplicated)", checkoutCount)
 }
+
+// TestDuplicateStepValidation_CheckoutPlusGitHubApp_Integration tests that combining
+// a top-level github-app with multiple cross-repo checkouts and tools.github does not
+// produce duplicate 'Generate GitHub App token' steps in the activation job.
+//
+// When multiple checkout entries all fall back to the top-level github-app,
+// each minting step previously received the same name, triggering the duplicate
+// step validation error ("compiler bug: duplicate step 'Generate GitHub App token'").
+func TestDuplicateStepValidation_CheckoutPlusGitHubApp_Integration(t *testing.T) {
+	tmpDir := testutil.TempDir(t, "duplicate-checkout-token-test")
+
+	// Workflow that combines all three conditions that triggered the bug:
+	//   1. Top-level github-app: (used as fallback for all token-minting operations)
+	//   2. Two cross-repo checkout: entries (both fall back to the top-level github-app)
+	//   3. tools.github: with mode: remote
+	mdContent := `---
+on:
+  issues:
+    types: [opened]
+engine: claude
+strict: false
+permissions:
+  contents: read
+  issues: read
+  pull-requests: read
+
+github-app:
+  app-id: ${{ secrets.APP_ID }}
+  private-key: ${{ secrets.APP_PRIVATE_KEY }}
+  repositories: ["side-repo", "target-repo"]
+
+checkout:
+  - repository: myorg/target-repo
+    ref: main
+  - repository: myorg/side-repo
+    ref: main
+
+tools:
+  github:
+    mode: remote
+    toolsets: [default]
+---
+
+# Test Workflow
+
+This workflow tests that multiple checkouts + top-level github-app + tools.github
+compile without duplicate 'Generate GitHub App token' step errors in the activation job.
+`
+
+	mdFile := filepath.Join(tmpDir, "test-checkout-github-app.md")
+	err := os.WriteFile(mdFile, []byte(mdContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to create test file: %v", err)
+	}
+
+	// Compile workflow — must succeed so the generated lock file can be validated.
+	compiler := NewCompiler()
+	err = compiler.CompileWorkflow(mdFile)
+	if err != nil {
+		if strings.Contains(err.Error(), "duplicate step") {
+			t.Fatalf("Regression: duplicate step error when combining multiple checkouts + top-level github-app: %v", err)
+		}
+		t.Fatalf("Compilation failed unexpectedly before lock-file assertions could run: %v", err)
+	}
+
+	// Read the generated lock file and verify the activation job has unique step names
+	lockFile := stringutil.MarkdownToLockFile(mdFile)
+	lockContent, err := os.ReadFile(lockFile)
+	if err != nil {
+		t.Fatalf("Failed to read lock file: %v", err)
+	}
+	lockContentStr := string(lockContent)
+
+	// Both checkout token minting steps should be present with unique names.
+	// The step names are "Generate GitHub App token for checkout (N)" — one per checkout entry.
+	count0 := strings.Count(lockContentStr, "name: Generate GitHub App token for checkout (0)")
+	count1 := strings.Count(lockContentStr, "name: Generate GitHub App token for checkout (1)")
+	if count0 != 1 {
+		t.Errorf("Expected exactly 1 'Generate GitHub App token for checkout (0)' step, got %d", count0)
+	}
+	if count1 != 1 {
+		t.Errorf("Expected exactly 1 'Generate GitHub App token for checkout (1)' step, got %d", count1)
+	}
+
+	// Exactly one generic "Generate GitHub App token" step is expected — for the GitHub MCP server
+	// in the agent job (id: github-mcp-app-token). If more than one appears, that means a
+	// checkout minting step was not renamed, which would cause a duplicate-name error.
+	genericCount := strings.Count(lockContentStr, "name: Generate GitHub App token\n")
+	if genericCount > 1 {
+		t.Errorf("Found %d generic 'Generate GitHub App token' steps; checkout steps must use unique names to avoid duplicates", genericCount)
+	}
+
+	t.Logf("✓ No duplicate token steps: checkout (0) count=%d, checkout (1) count=%d, generic=%d", count0, count1, genericCount)
+}