Adjacent to the mosque is the still-active Fatima Khatun Girls' School.

[1][2] The existing structure was founded in 1566 by Fatima Khatun, the wife of Lala Kara Mustafa Pasha, the Bosnian governor of Damascus during the reign of Ottoman sultan Suleiman the Magnificent.

Fatima Khatun paid regular visits to the area, but took a particular liking to Jenin while traveling towards Jerusalem for pilgrimage.

[1] In the center of Jenin, she decided to have the building established atop the remains of the old mosque.

Numerous religious trusts (waqf) including a local public bath (hamaam) and many of the nearby shops were designated to fund the Fatima Khatun Mosque thereafter.