In a medium, heavy saucepan, heat the olive oil over medium heat. Add the onions, salt, and pepper. Cook, stirring occasionally, until the onions are tender, about 10 minutes. Add the thyme and broth. Simmer, uncovered, until the onions are soft, about 15 minutes.
Divide the soup between the 4 ovenproof ramekins. Divide the cubed bread among the ramekins. Top each with slices of fontina cheese. Place under the broiler, until the cheese is golden and bubbly, about 4 minutes. Serve immediately.