Trim the fennel bulbs and split lengthwise. Boil until tender, about 15 minutes. Drain, cut side down, on paper towels for about 5 minutes.
Place fennel, cut side up, in a buttered baking dish and brush with the softened butter. Season with the salt and pepper and top with thyme and grated Parmesan. Bake until cheese is golden brown, about 20 minutes