Preheat the oven to 375 degrees F (190 degrees C). Lightly grease a casserole dish.

Bring a large pot of salted water to a boil. Add shell pasta and cook, stirring occasionally, until tender yet firm to the bite, about 9 minutes.

While the pasta is cooking, melt butter in a small saucepan over medium-low heat. Whisk in flour and stir until mixture becomes paste-like and light golden brown, 2 to 4 minutes. Gradually whisk in milk, salt, and pepper, then bring to a simmer over medium heat. Gradually whisk in shredded cheese; cook, whisking constantly, until sauce is smooth and thick enough to coat the back of a spoon, 5 to 10 minutes.

Drain pasta and transfer to a large bowl. Pour cheese sauce over top and mix until thoroughly combined. Transfer to the prepared casserole dish.

Bake in the preheated oven until heated through, about 15 minutes.