Cook pasta according to package directions; drain.
Melt butter over low heat. Mix in flour and stir until smooth; remove from heat.
Add milk slowly. Return to heat and cook, stirring constantly until mixture comes to a boil and thickens, approximately 5 minutes.
Remove from heat and add mustard and cheese, reserving 1/4 cup of the Cheddar. Stir until cheese is melted.
Season with salt and pepper.
Mix in cooked macaroni. Pour into prepared dish. Top with reserved cheese.
Bake at 350 for 20-30 minutes.