The church goes by several names, which is what happens when a building survives a thousand years. Locals call it the Russian Church. The Greek state knows it as Soteira Lykodimou; modern usage often corrupts that to Saint Nikodemos, although there is no Saint Nikodemos involved. Lykodemos was probably the family name of a founder. In the nineteenth century the Greek archaeologist Kyriakos Pittakis tried to argue that Lykodemos derived from the classical Lyceum of Aristotle, which would have placed Aristotle's school somewhere underneath. The theory was tempting but never proved, and in 1996 archaeologists found the actual site of the Lyceum about a kilometer to the east. What the excavations beneath the church did reveal, though, was a sixth-century basilica: when the Byzantine masons broke ground here in the eleventh century, they were already building on top of older sacred ground.

Among Byzantine churches in Athens, this is the largest one still standing. It is also, in the words of architectural historians, the earliest and most faithful copy of the great katholikon of Hosios Loukas - the famous monastery near Delphi that was completed in 1011. The dimensions of the Athens church are almost exactly three-quarters those of Hosios Loukas, scaled down by a careful hand. The plan is a cross-in-square with the dome resting on an octagonal base, the typical solution of middle Byzantine architecture. The masonry is high quality: dressed stones separated by double courses of brick, with pseudo-Kufic decorative panels worked into the walls. A graffito inside the church names a certain Stephen as the protoktetor, the first founder, and dates the building to before 1044, possibly before 1031. After that, the historical record goes quiet for five hundred years.

The church was originally the katholikon - the principal church - of a much larger convent. In 1778 the Ottoman governor of Athens, Hadji Ali Haseki, tore down the rest of the convent for stone to build new city walls. By the sixteenth century the surrounding area had been abandoned, according to the nineteenth-century Russian archimandrite Antonin, and only the church remained occupied. The earthquake of 3 September 1705 caused enough damage that the interior had to be repainted. Then came the 1821 siege of the Acropolis, when Greek revolutionaries were trying to dislodge the Ottoman garrison perched on the rock above and the Ottoman defenders were firing back into the city below. A cannonball found the dome. The war ended in 1829 with Greek independence, and the church sat in its rubble for nearly two decades while the new state had no money for it.

Tsar Nicholas I made the offer in 1847. Russia would pay to restore the church if Greece would let the growing Russian Orthodox community in Athens use it for services. The Greek government agreed on one condition: the building had to be returned, as closely as possible, to its original Byzantine form. From 1850 to 1855, under the supervision of Greek Army major T. Vlasopoulos, masons rebuilt the dome, the western side, and almost all the vaults, while keeping the eastern wall and most of the north and south sides as the original Byzantine fabric. The restoration was not a perfect one. At the urging of the French scholar A. Couchaud, Vlasopoulos removed all the interior non-bearing walls in pursuit of an imagined original purity, and some of those walls had been integral to the eleventh-century plan. The marble templon was carried off and never restored. The German artist Ludwig Thiersch painted the interior frescoes that visitors see today, working with Greek collaborators Nikiforos Lytras and Spyridon Hatzigiannopoulos. The eleventh-century paintings are gone except for a single bust of Christ and two angels on a southern arch.