The name of this subterranean structure derives from a large public square on the First Hill of Constantinople,
the Stoa Basilica, beneath which it was originally constructed. Before being converted to a cistern, a great Basilica stood in its place, built between the 3rd and 4th centuries during the Early Roman Age as a commercial, legal and artistic centre. The basilica was reconstructed by Illus after a fire in 476.

Ancient texts indicated that the basilica contained gardens, surrounded by a colonnade and facing the Hagia Sophia. According to ancient historians, Emperor Constantine built a structure that was later rebuilt and enlarged by Emperor Justinian after the Nika riots of 532, which devastated the city.

Historical texts claim that 7,000 slaves were involved in the construction of the cistern.

The enlarged cistern provided a water filtration system for the Great Palace of Constantinople and other buildings on the First Hill, and continued to provide water to the Topkapi Palace after the Ottoman conquest in 1453 and into modern times.