The building was originally a Roman Catholic church erected in 1325 by the friars of the Dominican Order, near or above an earlier chapel dedicated to Saint Paul (Italian: San Paolo) in 1233.

It was later given by Sultan Bayezid II to Muslim refugees from Al-Andalus who escaped the Spanish Inquisition in 1492 and settled in the Galata neighborhood of Istanbul (hence its current name, Arab Mosque).

[1] The tradition which affirms that a mosque was built on this site during the Second Arab Siege of Constantinople in 717–18 by the Umayyad prince and general Maslama ibn Abd al-Malik is a later, Ottoman-era legend.

[11] Towards the end of the century Sultan Bayezid II assigned the building to the Muslim of Spain (Moriscos) who had fled the Spanish Inquisition and migrated to Istanbul; hence the present name Arap Camii (Arab Mosque).

[1][10] Sultan Mehmed III repaired the building, and towards the end of seventeenth century the houses which encroached upon the mosque were pulled down in order to avoid noise.

[13] After another fire in 1808, in the mid-nineteenth century, the daughter of Mahmud II, Adile Sultan, repaired the mosque again and in 1868 built a şadirvan (fountain for ritual ablutions before praying) in the courtyard.

[2] The Gothic-style portal, lancet windows and the prominent bell tower (which has been transformed into a minaret by the addition of a conical roof) distinguished the building from the Byzantine churches in the city.

It is one of the most interesting mosques in the city due to its early Italian Gothic architectural style and church belfry, which has practically remained unaltered even after being converted into a minaret.