[1] The mosque was built in 1347 on the orders of the emir ("prince") Shams ad-Din Aqsunqur during the reign of the Mamluk sultan, al-Muzaffar Hajji.

[2] Medieval Muslim historian al-Maqrizi noted Aqsunqur supervised the entire project and also participated in its actual construction.

[2][3] By the 15th century the Aqsunqur Mosque was reportedly in poor shape due to the loss of waqf ("religious endowments") funds from Syria.

[3] The tiles, which were imported from Constantinople and Damascus,[4] were crafted in the Iznik style with floral motifs such as cypress trees and vases holding tulips.

The 1992 Cairo earthquake damaged the arches of the mosque's porticoes, but they were reinforced by the Egyptian government in the mid-1990s to prevent additional deterioration.

[5] The Aga Khan Trust for Culture (AKTC) in conjunction with the World Monuments Fund began a restoration project of the mosque in 2009.

[6] The general layout of the mosque consists of a large open courtyard (sahn) enclosed by four arcades (riwaqs).

[7] The mosque's interior also has an irregular layout mostly due to Ibrahim Agha's renovations which replaced most of the original cross-vaulting of the arcades with columns supporting a flat wooden ceiling.

The only part of the mosque that continues to employ Aqsunqur's interior design is the qibla wall which uses cross-vaults that rest on octagonal-shaped piers.

[3] The mihrab ("prayer niche" that indicates qibla) was built in a geometric interlace style typically found in Mamluk architecture.

Decorated with light gray, salmon, green and plum-colored stone inserts, it is the oldest and one of the handful remaining marble minbars used in a Cairo mosque.