Preheat oven to 425°F. Heat olive oil in a large skillet over medium heat. Add the onion and garlic and cook until softened, about 5 minutes. Stir in the balsamic vinegar, salt, and pepper and cook for another 3 minutes.
Place the naan flatbreads on a baking sheet. Spread each with 1/4 cup of marinara sauce and top with 1/3 cup of cheese. Divide the caramelized onions between the three pizzas.
Bake for 10-12 minutes or until cheese is melted and bubbly. Serve hot.