Saskatoon 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 Saskatoon Presbytery, which had been part of the Presbyterian Synod of Saskatchewan. Prior to Union, in 1925, there had also been a Saskatchewan District, in the Saskatchewan Conference of the Methodist Church.

In 2000, Saskatchewan Conference went from 10 presbyteries to 7, with each adopting a new name. Most pastoral charges from Saskatoon Presbytery became part of the new River Bend Presbytery.