The river begins at the outflow of an unnamed lake at an elevation of and flows west into Sussex Lake, then north to Muskox Lake, at the border between the Northwest Territories and the Kivalliq Region, Nunavut, where it takes in the left
tributary Icy River. It flows over the Muskox Rapids, takes in the
left tributary Contwoyto River, and heads east through the Heywood Range. The Back River heads over the Malley Rapids, takes in the left tributary Siorak River and enters the long lake-expansion
Lake Beechey in a southeast direction. It heads east, takes in the right tributary Baillie River, left tributary Warren River, right tributary Jervoise River, passes over the Hawk Rapids, takes in the right tributary McKinley River and right tributary Consul River. Between the Baillie and Consul Rivers, the Back River forms the northern border of the
Thelon Wildlife Sanctuary. The river turns northeast, takes in the left tributary Bullen River, and reaches Pelly Lake at an elevation of . It flows east through, in immediate succession: Upper Garry Lake, where it takes in the right tributary Morse River;
Garry Lake; Lower Garry Lake; Buliard Lake; Upper MacDougall Lake; and Lower MacDougall Lake. The Back River then heads over the Rock Rapids, Sinclair Falls, Escape Rapids, Sandhill Rapids, and Wolf Rapids, and takes in the right tributary Meadowbank River. The river curves around Mount Meadowbank, takes in the right tributary Hermann River and left tributary Montresor River, passes McKay Peak, heads over the Whirlpool Rapids, and reaches Franklin Lake. It continues northeast, takes in the right tributary Mistake River, passes north into Kitikmeot Region, takes in the right tributary
Hayes River and reaches its mouth at Cockburn Bay on
Chantrey Inlet on the Arctic Ocean. ==Watershed==