The brick rotunda went up in the early fourth century, when this city was Serdica, capital of the Roman province of Dacia Mediterranea, and an imperial residence important enough that Constantine reportedly considered making it his eastern capital before settling on Byzantium. It was likely built as part of a larger Roman complex, probably for use as baths, and it sits in what archaeologists call the Constantine district, near the foundations of an imperial palace. The dome rises 13.7 meters above a square base, a circle inscribed in a square, four niches softening the corners. From the late fourth century onward Christians were using the building for baptisms. By the time the Council of Serdica gathered in 343 to argue about the divinity of Christ, this was already a sacred room, and tradition holds that some of those debates happened inside its walls.

Five layers of fresco have been identified on the interior. The deepest is Roman-Byzantine floral work from the fourth century, faint but legible. Above that, tenth-century Bulgarian medieval painting from the golden age of the First Bulgarian Empire, when emperors Simeon, Peter, and Samuil ruled. Then eleventh and twelfth-century work showing prophets, the Ascension, the Assumption. Then a fourteenth-century donor portrait of a bishop near the entrance. Then, finally, ornamental Islamic motifs from the Ottoman centuries. Twenty-two prophets, each more than two meters tall, ring the dome. Among the medieval angels is a single face, painted around the year 1000, that art historians treat as one of the most expressive surviving examples of First Bulgarian Empire iconography. It is calm and unsentimental, looking out from a thousand years away as if waiting to see what you will do next.

For a stretch of the medieval period, the church held the relics of John of Rila, patron saint of Bulgaria. Legend says they were used to cure the Byzantine emperor Manuel Komnenos. In 1183, allied Serbian and Hungarian troops under Bela III of Hungary sacked Sofia and carried the relics off to Esztergom. According to one chronicle, the Catholic bishop there committed some unspecified indecency with them and lost the power of speech as punishment, after which the relics were quietly returned to the restored Bulgarian Empire in 1187. They eventually traveled from Tarnovo to the Rila Monastery in 1469, where they remain today. Stefan Milutin, the medieval Serbian king who was beatified after his death, was buried at the rotunda for a time before being moved to what is now the Sveta Nedelya Church.

In the sixteenth century, the Ottomans converted the rotunda to a mosque. The frescoes were painted over, the dome whitewashed, and for several centuries the building served Sofia's Muslim community. In the mid-nineteenth century it was abandoned along with several other former churches in the city, and after the Bulgarian liberation it returned to Orthodox use. Restorers in the twentieth century slowly removed the layers of plaster and uncovered the medieval frescoes underneath. Today the rotunda stands at the bottom of its courtyard with the modern presidency rising above it on one side and a luxury hotel on the other. Liturgy is celebrated again, occasionally classical concerts fill the dome with sound, and Sofia's oldest building goes on outlasting every authority that has ever tried to claim it.