Preheat oven to 350 F. Cook pasta according to package directions, drain. Melt butter in a large saucepan over medium heat. Whisk in flour and cook for a minute to brown.
Pour in milk and add in pepper jack cheese and 1 cup of shredded cheddar cheese. Season with salt and pepper. Continue to cook over medium heat, whisking constantly until smooth and thickened.
Mix the sauce with the cooked pasta and spread out into a large greased baking dish. Top with the remaining shredded cheddar cheese. Bake for 25-30 minutes.
