Bring a large pot of lightly salted water to a boil. Cook elbow macaroni in the boiling water, stirring occasionally until cooked through but firm to the bite, 8 minutes. Once cooked, drain them.
Melt butter in a saucepan over medium heat; stir in flour, salt, and pepper until smooth, about 5 minutes. Slowly pour milk into the butter-flour mixture while continuously stirring until mixture is smooth and bubbling, about 5 minutes. Add half of the Cheddar cheese and the Gruyere cheese to the milk mixture and stir until cheese is melted about 4 minutes.
Fold the macaroni into the cheese sauce until coated.
Pour half of the mac and cheese into a baking dish. Top with the remaining shredded cheese and then the remaining mac and cheese.
In a small bowl, combine the gluten-free breadcrumbs, parmesan cheese, melted butter, and paprika. Sprinkle over the top and bake until bubbly and golden brown, about 20 minutes. Serve immediately.