Bring a large pot of salted water to a boil and cook the penne according to package directions until al dente.
While pasta is cooking, heat 1 tablespoon of olive oil in a large skillet over medium-high heat.
Add the Italian sausage to the skillet, breaking it into crumbles with a spatula, and cook until browned and cooked through (about 7-8 minutes). Remove sausage from skillet and set aside.
Add the remaining 2 tablespoons of olive oil to the same skillet. Place Brussels sprouts cut-side down and cook undisturbed for 4-5 minutes until caramelized and golden brown.
Add the diced onion and minced garlic to the skillet with the sprouts; sauté for 2-3 minutes until onions are translucent.
Return the cooked sausage to the skillet and stir in the red pepper flakes, salt, and black pepper.
Drain the pasta, reserving 1/2 cup of the cooking water.
Add the pasta and reserved water to the skillet, tossing constantly over medium heat until a light sauce forms and coats the pasta.
Remove from heat, stir in the parmesan cheese, and serve immediately.