The river has its sources in the Pamir Mountains in Gorno-Badakhshan province in the far eastern part of Tajikistan. It flows between the Wakhan Range (south) and the Southern Alichur Range(north). It starts from the Lake Zorkul, at a height of 4130 meters, and then flows towards the west, and later southwest. Near the town of Langar, at 2799 m, it joins the Wakhan River and forms the Panj River. The Pamir forms the boundary between Tajikistan and Afghanistan along its entire length. Northwest of Langar is the high Karl Marx Peak and Friedrich Engels Peak (). A road runs along the river on the Tajik side to Khargush where it turns north to join the Pamir Highway. A road of lower quality continues east past Zorkul, almost to the Chinese border.