	Baker Run begins on Stone Mountain in Noxen Township. It flows south-southeast down the mountain for a few tenths of a mile before turning south and continuing to flow down the mountain. After a short distance, it enters a deep valley and receives Windfall Run, its only named tributary, from the right. The stream then turns southeast for a short distance before turning south for a short distance. It then heads in an east-northeasterly direction (although it makes several turns) for a few tenths of a mile before reaching its confluence with Bowman Creek.