The present building dates from 1904 and was designed by the architect Carl Möller, replacing an earlier wooden chapel that had served the poorer district then known as Sibirien. That original chapel was later dismantled and moved to Aspudden, where, renamed Sankt Sigfrids kyrka, it survives as a listed building.
Stefanskyrkan is built on a north-south axis with the chancel facing north and the main entrance through a tower set to the south-west. Its pale, tooled sandstone façades and pointed, late-Gothic-style window tracery recall medieval English parish churches, though the low tower and some detailing also show touches of Art Nouveau influence fashionable at the time. On the south gable is a stone crucifix carved by the sculptor Carl Eldh.
Inside, whitewashed walls and an unpainted timber floor sit beneath an open, decoratively carved roof structure. The chancel is dominated by a triptych altarpiece added during a 1926 remodelling overseen by Isak Gustaf Clason, its ten painted scenes by Einar Forseth depicting the Passion, Resurrection and Ascension. The church's earliest altar cross, thought to have been designed by Carl Eldh, dates from 1904; its iron cross now stands in the memorial garden at St Johannes churchyard.
Much of the current woodwork, including pews and a dividing screen creating an entrance vestibule, was introduced in later twentieth-century renovations, along with stained glass by Bengt Inge Lundkvist and chandeliers designed by Knut Hallgren. A 2003 restoration removed plastic paint applied in the 1980s that had trapped damp in the walls, replacing it with breathable limewash. The church has had several organs over the years, including a mechanical instrument from 1960 and, more recently, a digital organ.