Adjust oven rack to upper-middle position and heat oven to 425 degrees. Line baking sheet with parchment paper.
Unfold pastry onto lightly floured counter. Roll pastry into 10-inch square. Transfer to prepared sheet. Lightly brush ½-inch border along edges of pastry with water; fold edges of pastry over by ½ inch.
Stir together onions and thyme. Spread onion mixture in even layer over pastry, avoiding raised border. Arrange tomatoes and goat cheese evenly over onions. Season with salt and pepper to taste.
Bake until pastry is puffed and golden brown, 20 to 24 minutes, rotating sheet halfway through baking.
Transfer tart to cooling rack and let stand for 15 minutes. Transfer to cutting board, slice, and serve.
