Preheat oven to 350°F (180°C). Place fennel and leeks in a single layer in a 13 x 9 in. (3 L) baking dish. Place thyme stems overtop, combine broth and lemon juice and pour over vegetables.
Cover with lid or foil and braise in the oven for 45 min. When the fennel is tender remove from oven, remove thyme stems and top with fresh thyme leaves before serving.