Assiniboia Presbytery was one of the original 16 presbyteries established by the first General Council of the United Church of Canada (June 1925), to be part of the new Saskatchewan Conference. Initial boundaries were based on the previous Assiniboia Presbytery, which had been part of the Presbyterian Synod of Saskatchewan.

The presbytery was divided and recreated several times, over the years. In 1926, it was split into Assiniboia Presbytery and the new Shaunavon Presbytery. In 1951, the two were reunited under the original name Assiniboia Presbytery. In 1959, the presbytery was divided along Highway 19: the western part was combined with Swift Current Presbytery, to become Cypress Hills Presbytery, and the eastern part was amalgamated with Weyburn Presbytery, under the name Assiniboia Presbytery.

In 1973, Assiniboia Presbytery was dissolved and its pastoral charges were divided between Moose Jaw Presbytery and Arcola-Estevan Presbytery (which became the new Souris Valley Presbytery).