The river has its source in the Hal-Urekchen, at the confluence of the Left Balygychan and Right Balygychan rivers of the Kolyma Highlands. It flows roughly northwards along the western flank of the Omsukchan Range. In its middle course there is the abandoned town of Verkhny Balygychan (Upper Balygychan). North of the town the Balygychan flows along a marshy intermontane basin where the river widens, meanders and divides in arms. Finally it joins the right bank of the Kolyma from its mouth.