The original building was constructed by the Timurid general Mir Mazid Arghun[1] over the grave of Khawaja Abu Nasr Parsa, a local religious teacher and mystic of the Naqshbandi order.[2] Later on, Arghun's father and brother were buried there.[3] Arghun also constructed a madrasah next to the mosque. The mosque, shrine and madrasah complex was then put under the management of the descendants of Abu Nasr Parsa.[4] The Shaybanid governor of Balkh, Abdul-Mo'min bin Abdullah Khan, later renovated the building in the late 16th century, inscribing his name on one of the walls as well.[5]

The mosque suffered severe damage during the Soviet-Afghan War, and it fell into massive disrepair. In 2022, an explosion inside the mosque caused the destruction of some parts of the mosque as well.