Preheat oven to 350 degrees F and grease a 9x13 inch baking dish.
Cook the macaroni according to package directions in heavily salted water until al dente, then drain well.
In a large saucepan, melt butter over medium heat, whisk in flour, and cook for 1 minute to create a roux.
Gradually whisk in the whole milk until smooth, cooking until the sauce thickens slightly, about 5 minutes.
Remove from heat and stir in the Sharp Cheddar cheese, Gruyere cheese, salt, and black pepper until completely smooth.
Fold the cooked pasta into the cheese sauce until evenly coated, then pour the mixture into the prepared baking dish.
Sprinkle the panko breadcrumbs evenly over the top and bake for 30 minutes until golden and bubbly.