Keeper, a member of the Norway House Cree First Nation, was born at Walker Lake, Manitoba. He was sent to Brandon for schooling at the Brandon Indian Residential School, and it was while there, at high school, that he showed an enthusiasm for long distance running.
In 1912, he was selected to the Canadian Olympic team, and participated at the 1912 Summer Olympics at Stockholm, Sweden. He raced in the 5000 metre run and in the 10,000 metre run, where he finished fourth, the best result ever for a Canadian runner in that event.
In 1916, Keeper joined the Army, and served for two years in France. He received a Military Medal for his actions during the war . In 1917, Keeper joined with Tom Longboat to win an inter-Allied cross country championship near Vimy Ridge. Longboat, Keeper, and other First Nation long-distance runners A. Jamieson and John Nackaway served as despatch carriers for the 107th Pioneer Battalion. 
Following the war, he returned to Winnipeg, where he worked as a carpenter, before moving back to the northern part of the province, where he worked for the Hudson's Bay Company until he retired in 1951. He and his wife Christina McLeod  had four sons and three daughters. His granddaughter is actress and Canadian politician Tina Keeper.
The Joe Keeper Memorial Run (now the Joe Keeper - Angela Chalmers celebration run) is held each spring by the Manitoba Runners’ Association.. The Norway House Cree Nation holds memorial races in Keeper's name. 
- Joe Keeper entry at the Manitoba Sports Hall of Fame website
- Dewar, J. D. Joe Keeper: Runner of the Northwest (.pdf file)
- Kidd, Bruce The Struggle for Canadian Sport , ISBN 0-8020-7664-5
- Miller, James Rodger, Shingwauk's Vision: A History of Native Residential Schools, ISBN 0-8020-7858-3