The congregation's origins trace back to 1852, when three Uppsala students began holding informal meetings to discuss spreading Christian teaching more widely within the Church of Sweden—at a time when lay-led gatherings without a priest present were forbidden. This lay initiative was characteristic of what would become EFS, formally established from the Uppsala Mission Society founded in 1856. A split in the wider mission movement in the 1870s led to further reorganisation, and it was not until 1944 that a new EFS-affiliated mission society took shape, eventually growing into the congregation that built Lötenkyrkan.
By the early 1950s the growing society needed larger premises, and after using various borrowed spaces, including a chapel belonging to Uppsala Cathedral parish, it settled on a plot at Heidenstams torg in the new Löten district. EFS also chose to relocate its theological college, Johannelunds teologiska högskola, next to the new church. The first church building, designed by architect Henry Åkesson, was completed in 1970, alongside a formal cooperation agreement with Gamla Uppsala parish.
Within a few years the original building proved too small for the expanding congregation, and a larger church was built on the same site to designs by Per-Olof Gradin, opening in 1986. The earlier 1970 building was taken over by Johannelunds teologiska högskola, later serving as its library until 2018, after which it became home to the EFS national office.
The present church is a three-aisled basilica, its taller central nave flanked by lower side aisles, oriented north–south with the entrance to the north and the chancel to the south. A freestanding concrete bell tower of open construction stands just northeast of the church, added in 1991; its bell weighs 888 kilograms.
The church's mechanical organ was built in 1973 by Grönlunds Orgelbyggeri of Gammelstad and stands on a platform against the north wall. A smaller choir organ, built in the early 1980s by Birger Forsberg together with a local organ-building study group, incorporates pipework originally from an older organ in Uppsala Cathedral dating to 1928.