In a skillet, melt 2 tablespoons of butter over medium heat. Add sliced onions and cook, stirring occasionally for about 20 minutes until golden brown and fragrant.

Cook macaroni according to package instructions until al dente. Drain and set aside.

In a pot, melt remaining butter over medium heat. Whisk in flour until bubbly, then gradually add milk while whisking until thickened (about 5 minutes).

Stir in shredded cheddar and Gruyère until melted. Season with salt and pepper.

Mix cooked pasta into the cheese sauce; fold in caramelized onions gently.

Transfer to a greased baking dish, sprinkle panko on top, and bake at 350°F (175°C) for about 20 minutes until golden brown.