Preheat the oven to 375°F. Arrange the oven rack within the upper third of the oven so the casserole can develop an evenly browned surface when it is broiled later.
Bring a large pot of generously salted water to a full boil. Add the penne and cook it for 2 minutes less than the cooking time stated on the package. The pasta should remain slightly underdone because it will continue cooking in the oven.
Drain the penne thoroughly, then place it back into the pot.
Add the marinara sauce along with approximately one-third of the pepperoni slices. Stir until the pasta is evenly coated and the pepperoni is distributed throughout the mixture.
Transfer the sauced pasta into a 9 × 13-inch baking or casserole dish. Spread the mixture into an even layer to promote consistent heating.
Scatter the shredded mozzarella evenly across the entire surface of the pasta.
Place the remaining pepperoni slices over the mozzarella, distributing them across the top.
After the baking period, change the oven setting to broil. Broil for a few minutes, watching carefully, until the mozzarella develops light golden-brown areas and the pepperoni becomes slightly crisp around the edges.
Carefully remove the finished pizza pasta bake from the oven. Allow it to stand for a few minutes before portioning and serving so the hot cheese and sauce can settle slightly.