Established in 1965 as Algoma College, Algoma University was initially an affiliate of Laurentian University in Sudbury. In 1967, Algoma College began offering classes in portable building located at the Cambrian College site, now Sault College site. Algoma College moved into its current location, the former Shingwauk Residential School building, in 1971.

Former students of the Shingwauk Residential School formed the Children of Shingwauk Alumni Association and have helped guide the development of education on the Shingwauk site.  A provincial trust, the Shingwauk Education Trust, gives ownership of a portion of the site to Anishinaabek people, and Shingwauk Kinoomaage Gamig (SKG) has developed as an Anishinaabek institution for university studies on the site. Algoma signed a Covenant (PDF) in 2006 with SKG to work together for the benefit of all students of Algoma and Shingwauk.

In 2008, Algoma University was granted its charter and with the charter, achieved full autonomous university status as Ontario’s 19th University. Algoma University now offers over 30 academic programs in a diverse range of fields and through three faculties: Faculty of Sciences, Faculty of Social Sciences and Faculty of Humanities.