The history of the Christian Church in Moose Factory goes back to 1840 with the English Wesleyan Society. At the invitation of the Hudson's Bay Company, the Reverend George Barnley (a Wesleyan Minister) made his way to Moose Factory where he stayed for eight years. Strangely, when he left the community, no replacement was sent from the Wesleyans. It was then that the employees of the Hudson's Bay Company sent a letter to an Anglican Bishop requesting that a priest be sent to them to continue the work. So on June 8, 1851, John Horden sailed to the shores of James Bay arriving at Moose Fort on August 26 of that same year.

In 1864 construction began on an Anglican Church. The building was completed in 1885 and came to be known as St. Thomas' Anglican Church. It was a truly glorious building and was now to become the new spiritual home to the Anglican population of Moose Factory. And a spiritual home it was with as many as five Services every Sunday. Using the syllabic system developed by John Evans, John Horden (who later became the first Anglican Bishop of the Diocese of Moosonee) managed to translate much of the Old Testament, the Book of Common Prayer and many hymns into the Cree language. This made it possible for the Cree speaking people to participate in the Church Liturgy.

St. Thomas' Church has for many years served the needs of the people of Moose Factory. To this day, hymns are sung, prayers and lessons are read in the mother tongue of the Cree. In Moose Factory, the ministry of the church is not something of the past but continues with the same vibrancy with which it began.