It is located in the Brensholmen area on the western part of the island of Kvaløya.

It is the church for the Hillesøy parish which is part of the Tromsø domprosti (arch-deanery) in the Diocese of Nord-Hålogaland.

Originally, Hillesøy Church was located on the island of Hillesøya, just west of Sommarøy, about 6 kilometres (3.7 mi) south of the present church site on Kvaløya island.

A site at Brensholmen on the western coast of Kvaløya island was chosen.

It was about 6 kilometres (3.7 mi) south of the old church site.