In Fatih district at Zeyrek on İbadethane Street overlooking the Golden Horn, this building, used as a mosque today, was originally the Church of the Pantokrator Monastery bulit by Eirene, the wife of loannes II Kommenos and was one of the largest monasteries of İstanbul. Construction was completed in 1136. During the Latin invasion it was seized by Roman Catholic priests.

After the Ottoman conquest of 1453 Sultan Mehmed, the Conqueror had the monastry changed to a Islamic school and the church to a mosque. The first teacher was Molla Zeyrek Mehmed Efendi, the school and mosque taking his name.

It underwent serious repairs at the end of the 18th century. Having been in disrepair for many years, restoration work was started in 1966. There are three buildings all adjacent to each other. The roof is made up of five domes with a single gallery minaret. During restoration work the original floor was discovered and represents one of the best and rarest examples of the craftmanship of the 12th century.