The Pelly rises in glaciers on the western slopes of the Selwyn Mountains above in elevation, close to the Yukon-Northwest Territories boundary. It flows south and west through a wide valley, receiving many small tributaries from the east. It passes the Pelly Lakes, out of which flows the Woodside River, and there it turns to the west. The Pelly then assumes a northwesterly course through the Tintina Trench. It flows northwest to receive the Ross River at the town of Ross River where there is a cable ferry. Paralleling the Robert Campbell Highway, it then merges with the Lapie River from the left and passes the community of Faro which can be reached by a bridge. After Faro, it runs south of Rose Mountain and receives the Glenlyon River from the left.