Preheat the oven to 350 degrees F (175 degrees C). Grease a 2-quart casserole dish with cooking spray.
Melt 3 tablespoons butter in a medium saucepan over medium heat. Whisk in flour; cook and stir for 2 minutes.
Gradually stir in milk and bring to boil; cook and stir until thickened, 3 to 5 minutes.
Add Velveeta; cook and stir until melted, about 3 minutes. Stir in cooked macaroni.
Spoon mixture into the prepared dish; sprinkle with Cheddar cheese. Mix melted butter and cracker crumbs until combined; sprinkle over casserole.
Bake in the preheated oven until heated through, about 20 minutes.
