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.

Saskatoon Grace Pastoral Charge was formed 1925, as part of Saskatoon Presbytery and consisting of Grace United Church. Around 1968, Grace United amalgamated with Westminster United Church, to form Grace-Westminster United Church (and Pastoral Charge), in Saskatoon.

Saskatoon Westminster Pastoral Charge was formed 1925, as part of Saskatoon Presbytery and consisting of Westminster United Church. Around 1968, Westminster United amalgamated with Grace United Church, to form Grace-Westminster United Church (and Pastoral Charge), in Saskatoon.

Sutherland Pastoral Charge was formed 1925, as part of Saskatoon Presbytery and containing preaching points at St. Paul's United Church, in Sutherland, and Floral. Prior to union, St. Paul's had been a Presbyterian Church (built ca.1910), whose congregations had joined with local Methodists in the 1920s, after their church closed. After a fire, in 1943, the congregation worshipped for 3 years at Sutherland School (across the street), until the church was rebuilt. By 1951, the charge included Second Street United (Saskatoon) and Cory. Second Street returned to a separate charge ca.1955. In 1956, Sutherland became part of Saskatoon and around the same time the charge was renamed Saskatoon St. Paul's Pastoral Charge.

Saskatoon Third Avenue Pastoral Charge was formed as as a new United Church charge in 1925, under Saskatoon Presbytery. It closed June 30, 2018.