In a skillet, heat the olive oil over medium heat. Add the onions, thyme, 1 teaspoon salt and 1/2 teaspoon pepper and cook until the onions are softened, about 8 minutes.
Add the apple, lower the heat to medium-low and cook, stirring, until tender, about 10 minutes. Increase the heat to medium-high and cook until caramelized, about 10 minutes; season with salt and pepper. Serve warm.