Heat oven to 400º F. Heat the oil in a large skillet over medium heat. Add the onions and cook, stirring occasionally, until soft and golden brown, 12 to 15 minutes. Stir in the apples, ½ teaspoon salt, and ¼ teaspoon pepper and cook until just tender, 2 minutes.
Place each sheet of pastry on a parchment-lined baking sheet and prick all over with a fork. Spread with the crème fraîche, leaving a ½-inch border. Top with the onion mixture and bake until the pastry is crisp and browned, 30 to 35 minutes. Cut into pieces before serving.