Preheat oven to 350 F. Cook pasta according to package directions, drain and place into a large bowl. Melt butter in a large saucepan over medium heat. Add in flour and cook for a minute to brown.
Add in milk, cheese, salt, and pepper. Continue to cook over medium heat, while whisking constantly until thickened. Mix sauce with cooked pasta. Add in 1/2 of the fried onions.
Evenly divide mac and cheese mixture between 12 greased muffin cups. Top with the remaining fried onions. Bake for 15-20 minutes.
