The oldest parts of the church are thought to date from the later thirteenth century, when it was probably built as a private chapel for the nearby Finsta manor, likely on the initiative of the lawman Birger Persson, father of Saint Birgitta. This may explain the unusual proximity of two medieval churches, Skederid and Husby-Sjuhundra, only about two kilometres apart and within sight of each other.
The building's history is more complicated than its present rectangular form suggests. Originally a small church, it consisted only of what is now the sacristy and chancel, with the current sacristy serving as the original chancel. After a fire in the fourteenth century damaged the roof, it was rebuilt with wooden barrel vaulting. Following Birgitta's canonisation in 1391, Skederid became a pilgrimage church, and a larger nave was added to the west around the mid-fifteenth century, with brick vaulting following some decades later. The porch on the south side, later fitted out as a chapel with its own altar niche, was built before 1527. Because the old chancel continued in use, the church ended up with an unusually elongated interior. Traces of medieval wall paintings survive, including a scroll motif above the altar and consecration crosses in the chancel and sacristy.
By the eighteenth century the building had fallen into disrepair, prompting a major rebuilding between 1748 and 1749 (completed by 1767), during which the opening between the old chancel and nave was closed, the old chancel became the sacristy and the old nave became the chancel — effectively reversing the earlier arrangement. The walls were rendered and limewashed, the roof structure altered, and the current pews installed. Further changes followed in the nineteenth and twentieth centuries, including enlarged windows, the demolition of the old sacristy in 1880, and a 1923 restoration under architect Melchior Wernstedt.
A medieval stone gateway (stiglucka) stands at the churchyard entrance to the west, with a timber bell tower built above it in 1775–76 using timber salvaged from an earlier freestanding bell tower of 1692. Most of the church's medieval treasures, including a Lübeck-made altar shrine with a pietà from the 1470s, a thirteenth-century crucifix, a fourteenth-century apostle figure and an early fifteenth-century figure of Saint Birgitta, were sold in 1897 and are now held at the Swedish History Museum in Stockholm rather than in the church itself.
Objects that remain in the church include a seventeenth-century pulpit remodelled in the mid-eighteenth century, a silver communion vessel dated 1584 (other silver was stolen in 1839 and never recovered), and a composite altarpiece assembled in 1761–62 from paintings by Anders Eklund depicting the Crucifixion, with a further painting of Christ in Gethsemane added in 1831. The larger of the two church bells is said to date from the fourteenth century, and the organ case on the gallery dates from 1857, though the organ mechanism has been rebuilt several times since.