Bring water to a boil and cook pasta according to package directions. Pour into a strainer and put the empty pot back on the stove.
Turn the heat to medium and to the empty pot. Add butter and melt. Pour in flour and mix until combined.
Add milk, salt, and pepper and whisk frequently until it comes to a boil. Turn off the heat.
Add the cheese to the milk mixture and whisk until the cheese is completely melted and mixed in.
Add the drained noodles back to the pot and mix until every noodle is coated in cheese goodness!