Pernaja medieval stone church was built between years 1410 and 1440 to the place of previous wooden church. The interior was completed during centuries: there are for example a christening pool from the 1300s, a crusifix from 1400s and pulpit from the 17th century. Beautiful chalk paintings in walls are dated back to 1440s.
The first written record of church in Danmark locality date back to the year 1291. Close to the church are several stones with a Christian text and cross inscribed. The oldest parts of the present red-brick church are from the 1300s. In the late 1400s the church was enlarged to the appearance it has today. The church has been modified both internally and externally several times, among other things after the fires in 1699 and 1889. There are lot of well-preserved mural paintings in the walls.