Preheat oven to 400 degrees.
In a small bowl, combine melted butter, honey, lemon zest and thyme leaves. Set aside.
Place peach halves, cut side down in a glass baking dish. Pour honey mixture over peaches. Sprinkle on salt, pepper and red pepper flakes, to taste. Bake in preheated oven until just soft, about 10-20 minutes. (Cooking time may vary depending on how ripe your peaches are so start checking after 10 minutes).
Remove from oven and cool baking dish on a wire rack. Serve peaches warm or room temperature, drizzled with the sauce from the baking dish.