It is the church for the Selje parish which is part of the Nordfjord prosti (deanery) in the Diocese of Bjørgvin.

From the 12th until the 16th century, the old Selje Abbey was a major religious center for the region.

By the year 1340, the church was described by the archbishop as being in poor condition due to neglect.

By the mid-1500s, the small island was no longer inhabited and parishioners had to travel by boat to the church from the mainland.

Each church parish was a constituency that elected people called "electors" who later met together in each county to elect the representatives for the assembly that was to meet in Eidsvoll later that year.

The new church was designed by Frederik Hannibal Stockfleth and the lead builder was Rasmus Sætre from Stryn.

The new building was consecrated on 13 May 1866 by the Bishop Peter Hersleb Graah Birkeland.