The building began as a Byzantine church, its origins predating the Ottoman conquest of Constantinople in 1453. After the city fell, the church's conversion to a mosque was recorded by the eighteenth-century historian Hafiz Hüseyin al-Ayvansarayî in his work Hadîkatü'l-cevâmi' — a survey of Istanbul's mosques that remains one of the essential documents for tracing the city's religious architecture. According to Ayvansarayî, the conversion was carried out by İbrahim Ağa, who died in 1496 or 1497. İbrahim Ağa held the position of sekbanbaşı — lieutenant of the Ottoman sekban infantry regiments — and it was his title, rather than his name, that the mosque kept for the next four and a half centuries.

The building stood in Kendir Sokağı, in the Kırkçeşme quarter of the Fatih district, close to the massive Roman aqueduct that Valens built in the fourth century and that still strides across the city today.

The mosque's later history is a catalogue of misfortune. A fire in 1838 damaged it, but restorations followed and it continued to function. The second blow came in 1918, during the last years of the Ottoman Empire, when fire swept again through the mosque and its surrounding neighborhood. This time there were no repairs. The building was abandoned, its structure slowly deteriorating into the decade after the empire's collapse.

The decision that finally ended it came in 1943. The Turkish government was widening and modernizing Atatürk Boulevard, and the ruined foundation of the Sekbanbaşı Mosque stood in the way. It was demolished. By 1954, apartment blocks occupied the cleared ground. The mosque that had once been a church had become, in the end, nothing — not even ruins.

Just before the demolition of 1943, the archaeologist Semavi Eyice conducted a hurried excavation of the site. He uncovered and documented some of the mosque's substructures — the foundations and lower walls that held the memory of both the Ottoman mosque and the Byzantine church beneath it. The examination was done on the spot, in the window between the decision to demolish and the moment the machinery arrived.

Eyice's work gave the building something the fires had not taken: a record. The substructures were measured and surveyed, their findings entered into the scholarly literature. It is a thin kind of survival, but it is the only kind available. The Sekbanbaşı Mosque exists now as a set of measurements and a photograph from 1877, a ghost in the archives of a city too layered with history to preserve all of it.