Crystal Lake High School was established in 1976, to house Aboriginal girls sent there for their education. It was only accessible by float plane. In 1986, Stirland Lake and Crystal Lake High Schools merged operations, and Stirland Lake continued as a co-educational residential school for aboriginal children.

In October 2007, Windigo First Nations Council, supported by Nishnawbe Aski Nation (NAN), formally requested that Crystal Lake Residential High Schools be recognized under the Indian Residential Schools Settlement Agreement (IRSSA), following a resolution unanimously endorsed by NAN Chiefs-in-Assembly in August 2007. In the spring of 2008, the request for recognition by Windigo and NAN was rejected by Canada.

In December 2008, Windigo and NAN filed a motion to the Superior Court of Justice of Ontario, asking the Court to exercise its power under the IRSSA by adding the school to the list of recognized Indian Residential Schools within the meaning of the IRSSA. Written arguments were filed with the Court setting out the respective positions of Windigo and NAN, and also Canada, in great detail. Cristal Lake was added to the list of recognized residential schools in 2011.