Preheat oven to 400°F.
In a large pot, bring 2 quarts of water to a rolling boil. Add onions and cook for 30 seconds. Drain, and run ice cold water over the onions until cool. Cut off just the very tip of the root end and peel skin.
In a baking dish, arrange the peeled onions in a single layer. Drizzle on duck fat, sprinkle with salt and pepper. Add the thyme sprigs and toss until the onions are evenly coated.
Roast for 30-35 minutes, turning twice, until the onions are soft and caramelized.