Early Byzantine builders constructed the Balaban Ağa structure in a form that was unusual even for its era. The plan was circular on the outside — an outer diameter of 11.2 meters — but hexagonal within, each of the six interior sides bearing a deep rectangular niche. A rectangular apse extended from the south side. Surveys carried out before the demolition in 1930 found window-like openings in the rubble foundations, suggesting the presence of a crypt even in the building's earliest phase. Whether that crypt belonged to a mausoleum, a chapel, or something else entirely, no documentary record survives to say. In the fourteenth century, builders of the Palaiologan period added an almost square burial chamber measuring roughly 2.9 by 3.17 meters, covered with a flat dome. That addition effectively settled the question for later centuries: whatever the building had been before, it was now clearly a mausoleum, or at least serving that function. Traces of Palaiologan-era paintings were still visible on the walls when the demolition crews arrived in 1930.

Shortly after the fall of Constantinople to the Ottomans in 1453, the building was converted into a mosque by Balaban Ağa bin Abdullah, who held the position of Sekbanbaşı — chief of the Janissary corps — under Sultan Beyazid II. The endowment establishing the mosque as a religious foundation was registered in 1483. Conversion required adapting the old structure: the original entrance was blocked with masonry to accommodate a minaret, and a new entry was cut into the northwest side. A porch was added in front. The mosque gave its name to the surrounding quarter, which was known as Balabanağa. The neighborhood lay near the lodgings of the Janissary corps, a district called Eski Odalar — the Old Rooms — and the building found itself in a part of the city prone to fire.

Fire came to the Balabanağa quarter repeatedly: 1660, 1693, 1718. Each time, the small mosque was damaged and eventually patched back together. The great fire of 1782 partially burned the building, and the subsequent restoration changed its internal plan. By its final years the structure had acquired a wooden roof, five of its six interior recesses bearing windows and one serving as the entrance gate. The exterior showed four alternating sides, two curved and two projecting. A fire in 1911 dealt severe damage. The building limped into the twentieth century in poor condition, and when Istanbul city planners drew a new road — today called Harikzadeler Sokak — through the Fatih district, the old mosque sat directly in the way. The museum department carried out a brief architectural survey before demolition in 1930, recording dimensions and salvaging what fragments could be moved. The Byzantium 1200 digital reconstruction project has since produced a three-dimensional rendering based on those surveys, which is now the closest thing to a complete picture of what the building once looked like.

The architectural elements salvaged from the Balaban Ağa Mosque before its demolition are held at the Istanbul Archaeology Museum — stone and brick details that once formed part of the oldest surviving monument in the Balabanağa neighborhood. The street that replaced it, Harikzadeler Sokak, cuts through that same part of Fatih today with no visible marker of what stood there before. The Laleli Mosque and the Beyazit Mosque, both within walking distance, frame the area where the Balaban Ağa structure once occupied the middle of the road. That a building erect since the fifth or sixth century was lost not to war or earthquake but to urban planning speaks to how quickly the fabric of a city can be altered by ordinary administrative decisions. What no one can know is whether the building was a crypt, a library, or something else entirely — and now no one ever will.