According to the Gutasaga, a man named Likair (or Lickajr) the Wise built the first church in this district on his own farmstead. That early building was probably of timber, later replaced by one of stone — considered so unusual a material at the time that it gave both church and parish their name, Stenkyrka ("stone church"). No trace of this earliest structure has actually been found, and the various dates given for its origin, including a supposed year of 1032 and a claim tying its founder to the man buried in the choir in 1200, are uncertain and not well supported by sources.
The present building took shape gradually. The choir is thought to date from around the mid-1200s and was possibly the part consecrated in 1255, a date recorded for a Stenkyrka dedication in a medieval list of Gotland churches. The nave was rebuilt wider around 1270, and the tall tower that now dominates the surrounding landscape followed between about 1280 and 1310. The building is predominantly Romanesque in style, though the pointed Gothic forms of the west portal in the tower reflect the later phase of construction. The tower's spire was blown down in a storm in 1679 and, along with storm-damaged roofs, was not fully rebuilt until the early 1680s.
Inside, the church is notable for its extensive medieval wall paintings, uncovered during restoration in 1954–55 and dated to three main periods: quader (masonry-pattern) decoration and stylised foliage from the mid-1200s in the triumphal arch, marble-effect painting in the tower vaults from the later 1200s, and more elaborate figurative scenes from the close of the 1300s. The font, one of the oldest surviving objects in the church, is generally dated to around 1100–1200 and carries relief scenes from the life of Christ, along with faint traces of its original colouring.
Among the furnishings are a stone altar with consecration crosses cut into its corners, a carved sandstone altarpiece of 1688 (sources differ, with one attributing an earlier altarpiece painting to the 1660s), and a triumphal crucifix from the early 1300s now mounted on the north wall of the nave, having originally stood in the triumphal arch. The pulpit dates from the late 1600s, and the pews, in a Renaissance style with tall gable ends, are linked to the early 1600s and to later decorative painting attributed to Rasmus Bartsch around 1702.
The churchyard retains two stone stile-gates, in the north and east walls, thought to be medieval, along with a burial chapel that once served as the parish storehouse. Inside the church, two medieval gravestones in the choir floor are of particular interest: one commemorates a man named Licnatus of Stenstufu, carrying one of the earliest dated years known on a Gotland gravestone, and another honours a man named Jacob, shown in fine medieval dress with a pilgrim's hat suggesting a journey to the Holy Land, and his wife Botvid.