St. Thomas' origins date to the late 1840s when officials of the Hudson's Bay Company requested the bishop of the Anglican Diocese of Rupert's Land to send someone to continue the missionary work of the Rev.

The bishop sent an English schoolteacher, John Horden, who arrived on August 26, 1851, with his bride.

Horden set about learning the local Cree language and translating portions of the Bible, the Book of Common Prayer and hymns into it.

[1] In 2023, in conjunction with Moose Fort's 350th anniversary, the Moose River Heritage and Hospitality Association announced plans to restore St. Thomas' Church as a multipurpose community centre that can host church services as well as other civic and community events.

The association is hosting "reconciliation" talks among community members to address the legacy of St. Thomas' former residential school and the future use of the space.