Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente, about 10-12 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium-high heat.
Add the ground beef to the skillet and cook, breaking it apart with a spoon, until browned and cooked through, about 6-8 minutes. Drain excess fat if necessary.
Add the chopped onion to the skillet and cook until softened, about 3-4 minutes.
Stir in the minced garlic and cook for 1 minute until fragrant.
Pour in the crushed tomatoes and stir to combine.
Add dried oregano, dried basil, salt, black pepper, and red pepper flakes. Stir well.
Reduce heat to medium-low and let the sauce simmer for 10 minutes, stirring occasionally.
Add the cooked pasta to the skillet and toss to coat evenly with the sauce.
Remove from heat and sprinkle grated Parmesan cheese over the pasta. Stir gently to combine.
Garnish with chopped fresh parsley before serving.