The mosque was renovated at the turn of the 19th century by Veli Pasha of Ioannina and formed a complex consisting in particular of a madrasa and kitchens.

A first small mosque for daily prayer (masjid) was erected on the site of a Byzantine church dedicated to Saint Stephen,[1][2] to the south-west of the hill of Litharitsia,[3] about 500 meters from the Ioannina Castle.

[1] Ali Pasha of Ioannina, the semi-autonomous ruler of the Epirus region at the turn of the 19th century, had seraglios built in the area of the mosque for his first two sons, Mukhtar and Veli.

[9][11][12] Following the departure of Ottoman power in 1913 after Greece's annexation of Ioannina and the greater region of Epirus in the First Balkan War, the mosque became a barracks and its minaret was destroyed around 1930,[5] before being seized by the Greek Ministry of Culture and Sports.

[1][13] The madrasa of the mosque housed the city's Museum of National Resistance, but it was removed in 2021, and when the building was scheduled for restoration under the auspices of the Municipality of Ioannina.