After the Christianization of the Sami population of Inari, the first small church was built in 1647 in the winter village on the banks of Lake Pielpajärvi, where the semi-nomadic Sami people gathered during the cold season to trade and to settle their religious and legal affairs. The Swedish Queen Christina had the church named after herself and donated the bell and the priest's ceremonial robe. After the old church had been neglected for many years and had become dilapidated, the current church was built in its place between 1752 and 1760. The bell tower was added between 1760 and 1766. Around the church there were originally 30 to 40 church rooms in which churchgoers who had traveled from far away were accommodated, a rectory and several other buildings, none of which have survived. There was no cemetery, however, because the Sami traditionally buried the deceased on islands in Lake Inari. Around 1846, Pielpajärvi Church was renovated and given its current form.
When the Sami people settled in Inari, the winter village on Pielpajärvi was abandoned. After the village of Inari became settled, a new church was built there and Pielpajärvi Church was abandoned in 1888.