The church takes its name from S:ta Clara nunnery and convent church, founded here in the 1280s. Gustav Vasa had the medieval convent and its church demolished in 1527, though two altar cabinet doors from that earlier building are said to survive. The present church was built on the orders of Johan III in the late sixteenth century, with the Dutch master builder Hendrik van Huwen involved in construction; the royal architect Willem Boy may also have contributed to its design.
Built of brick on a Latin cross plan with a polygonal chancel and a west tower topped by a spire, the church has been reshaped by successive architects over the centuries, including Carl Hårleman, Carl Fredrik Adelcrantz and, in the twentieth century, Artur von Schmalensee. A fire around 1751 led to rebuilding the following year to Hårleman's designs, and the tower and façades gained much of their current appearance during a nineteenth-century restoration by Helgo Zettervall in the 1880s. The interior owes much of its present character to a further restoration in the early twentieth century, when painted decoration was added to the vaults.
At roughly 116 metres, the tower is often described as the second tallest church tower in Sweden and Scandinavia, after Uppsala Cathedral. It carries a carillon of 35 bronze bells, played manually from a small chamber inside the tower, alongside a separate set of older bells, two of which date from the mid-eighteenth century and two from the 1880s. Fittings inside the church include an altarpiece painted in 1766, an altar structure from the 1780s flanked by kneeling angels carved in the early twentieth century after an eighteenth-century original, a font from 1908, and a pulpit thought to date from the 1750s.
The churchyard, roughly the same size as it was in the seventeenth century, is now largely enclosed by later city buildings. It contains the graves of several notable Swedes, including the poet and composer Carl Michael Bellman and the poet Anna Maria Lenngren, among others associated with Swedish cultural history. A row of eighteenth-century burial vaults lines the southern edge of the churchyard, and a domed funerary chapel, designed in the late nineteenth century, stands among them. Archaeological work carried out when a nearby office building was constructed in the 1980s uncovered stone and brick cellar remains thought to date from the fourteenth century, associated with the original convent.
For many years the church has also been a base for practical outreach work in central Stockholm, including support for homeless people and others in difficult circumstances, coordinated with a local congregation and voluntary network.