Preheat oven 375°. In a large pot of salted boiling water, cook pasta according to package directions until al dente, less 2 minutes.

Meanwhile, in a large cast-iron skillet over medium-high heat, melt butter, whisk in flour, and cook for 1 minute. Add tomato paste and whisk in milk until smooth. Add oregano, red pepper flakes, and 1/2 teaspoon salt and bring to a boil. Simmer for 1 minute on medium heat.

Fold in half the cheese and add drained pasta. Top pasta with remaining cheese and sprinkle pepperoni all over.

Bake until pepperoni is crispy and pasta is bubbling, 10 minutes. Serve immediately.