It was built in the second half of the 15th century by Faik Pasha, first Ottoman conqueror of Arta. The mosque was built with materials that were transferred from the old Byzantine church of Consolation, from ancient Nikopolis and of several ancient buildings of Amvrakia.
According to archaeological findings, the mosque was probably built on the ruins of a Byzantine church dedicated to Saint John the Baptist.
The Faik Pasha, wanting to be forever immortalized his name in the area, decided to build imaret (workhouse) where he found shelter and food large number of poor people. Apart from the workhouse, the building complex surrounding the mosque included a madrasa, a caravanserai and a hammam. Because imaret, the area was named “Marathi”.
The mosque was theater of battles during the Revolution of 1821. According to John Makrigianni on November 14, 1821 Mark Botsaris fortified with 300 men in the mosque. With him in Marathi drafted several chieftains among them Georgios Karaiskakis. On November 15th, the Turks began incessant cannonade against Marat, caused significant losses to the Greek side and diverted to flee several soldiers. Mark Botsaris and Georgios Karaiskakis barricaded in the mosque and repulsed the attacks of the Turks until they appeared on the heights of Maratea, Notis Botsaris with 300 men and together drove the Turks to Arta.
After the liberation of Arta, the mosque was turned into a church dedicated to St. John the Russian. In 1938 by royal decree the mosque was declared a protected historical site.