The church is built on the former site of the 12th century Gilbertine Priory of Saint Katherine, which was originally located outside the Lincoln City walls. The site is alongside the Roman road Fosse Way. It was also the site of a Queen Eleanor cross, of which only a fragment remains at Lincoln Castle.

The current building was originally a Methodist Church, and opened on 4 October 1888. The architect was selected in a competition; the winner was Charles Bell, who proposed the development of the whole site including a school, which was built first. The church is orientated with the altar at the west end.

The church is built in brick with stone dressings and slate roofs, and consists of nave with clerestory and aisles, chancel, transept, and tower and spire to the south east. There is also an attached hall and associated buildings.

The nave is of four bays, the arcades are of polished granite. There is a gallery at the (ritually) west end. The chancel has a panelled dado and stained-glass east window which has currently been removed. The roof is arch braced with rafters and wall shafts. In the centre of the nave floor is a large glass panel exposing original mediaeval stonework beneath.

The pulpit was installed in 1903. The church steeple was added later and completed in 1908. The font was added around 1920.

Due to the high cost of maintenance the church was closed in 1976, and gradually deteriorated. In 2002 the Priory Trust was formed to restore the church, and it has now become the Saint Katherine's Heritage and Cultural Centre, with an associated Hall and Refectory. In 2013 the church was granted status of Cathedral as part of the Traditional Anglican church.