Bring a large pot of water to a boil, then add pasta. Cook pasta to manufacturer’s instructions. Transfer to a colander and drain well.
Melt butter in a 4-quart pot over medium heat. Whisk in flour and cook, stirring with a wooden spoon, until bubbling but not browning, about 45 seconds. Add milk and whisk to combine. Bring to a simmer, and continue to stir until smooth. Reduce heat to low and begin adding the cheddar cheese and fontina cheese in 1/2 cup increments. Let the cheese melt completely before adding more. Stir in 1/2 cup of Parmesan.
Taste the sauce and season with salt and pepper. Add pasta to sauce and stir to completely coat. Pour into a large baking dish. In a small bowl combine the remaining 1/2 cup Parmesan and the panko breadcrumbs. Scatter the mixture over the top of the baking dish.
Bake at 350 degrees for 20 minutes until top is golden and cheese is bubbly.