Preheat broiler. With a sharp knife scoop out the pulp from each tomato. Set tomatoes aside.
In a small bowl, combine the Queso Fresco, red onion, cilantro, salt, and pepper. Fill each tomato with a ¼ of the mixture. Place the tomatoes on a baking dish and place 6 inches under the broiler until the tomatoes are softened and the cheese is melted about 4 to 5 minutes.