The church was founded as the convent church for Cistercian nuns who moved from an earlier church at nearby Flasta in the 1230s. Building work began around the mid-thirteenth century, and the high altar is recorded as having been consecrated in the 1280s, with the nuns apparently transferring here around that time. A fire towards the end of the century led to further building work, including the vaulting seen today, and the church was reconsecrated around 1300.
Further major works followed in the late fifteenth century, and after the Reformation the building fell into disrepair until a renovation was funded by Herman Wrangel in the 1620s, which altered the roofline and added a small tower. A nineteenth-century restoration under the architect Emil Langlet uncovered the brick facades beneath later limewash, moved the entrance and added decorative wall paintings, giving the building much of its present appearance.
The church is built as a three-aisled brick basilica, considered one of the most important examples of the brick churches of the Mälaren valley. The former convent buildings have long since disappeared, though the ruins of the earlier Romanesque church at Flasta survive on a hill to the north-west. A free-standing bell tower from the eighteenth century stands near the south-west corner of the church, and the Wrangel family burial chapel adjoins the south side of the choir.
Among the church's furnishings are medieval wooden sculptures, including an oak crucifix and cross dating from the mid-1200s, a bishop figure, an oak Christ's head from the fourteenth century, and a Madonna and Child associated with a workshop possibly on Gotland. The elaborate altarpiece, pulpit and font are said to have come originally from the Oliwa monastery church in Poland, brought to Sweden and later given to Skoklosters kyrka by Carl Gustaf Wrangel in 1674.
The church also has two organs of note: a mechanical pipe organ built in 1804, and an older positive organ believed to date from a 1667 instrument supplied to Wrangel, which has passed between several churches over the centuries before being returned to Skoklosters kyrka and restored in the 1960s. Four rune stones stand near the church, including one carved with a spear-bearing rider on horseback.