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

The nave is supported by 22 staves (large bearing columns), eight on each of the longer sides and three on each of the shorter.

Historically, the church was thought to have been built in the late 12th century after the Battle of Fimreite, however recent research has changed this date.

Kaupanger was a market town that King Sverre burned down in 1184 to punish the local inhabitants for disobeying him.

It was previously thought that the second stave church (built in the early 12th century) burned down in this fire.

Also, around that time, the covered corridor that encircled the church was removed and some small windows were added to the nave.

In 1984, composer Arne Nordheim was inspired by the neumes and the sound of the medieval bells in Kaupanger stave church in composing the work Klokkesong, which was first performed inside the church as part of the 800th commemoration of the Battle of Fimreite.