Başdurak Mosque, like Şadırvan(altı) and Kestanepazarı Mosques, was built along the shores of the inner harbor. The mosque’s construction inscription has not survived, but the earliest known information about it is found in Evliya Çelebi’s Seyahatname. According to this source, the mosque was built in 1652, and its patron was Hacı Hüseyin Ağa. However, neither Seyahatname nor other historical sources provide further details about Hacı Hüseyin Ağa. Until the mid-19th century, the mosque was referred to as Hacı Hüseyin Ağa Mosque, but later, it became known by the name Başdurak, after the location where it stands.
Başdurak Mosque, like Şadırvan(altı) Mosque and Kestanepazarı Mosque, is a fevkani, with shops on the ground floor. These shops are still actively used today.