The Khanqah of Sultan Baybars II locates in El Gamaliya Street Facing a small Sabil and Kuttab that was constructed by Qitas Bey in 1630. This is one of the oldest and the earliest Khanqahs in Cairo to be attached with a royal tomb. The place of this Khanqah was earlier occupied with a palace from the Fatimid period and there are still few remains of the façade of the mausoleum that was included in the palace. This Khanqah was established by Baybars El-Gashankir who played an influential role in deposing the Sultan El-Nasir Mohammed by the assistance of Emir Salar and then both of them ruled Egypt for a while.

He served as the Atabek of Egypt and after the death of Emir Salar, he became the Sultan of Egypt in 1309. One year later, Sultan El-Nasir regained his power and came back to Egypt and took his revenge from Barsbay by torturing and then hanging him. Barsbay completed the construction of this Khanqah in the last year for him in power and spent a lot of money on its decoration. The beauty of the façade of this Khanqah is accentuated by the doorway that is supported with round arches. It is handsomely ornamented with S-curved forms, columns with nice shell niches, and windows with charming motifs and keel-shaped frames. This façade was once ornamented with beautiful tiles and the name of Baybars but most of it was erased by the order of Sultan El-Nasir. Of special interest in the Minaret of the Khanqah is the balcony that is supported with stalactites and the Mabkhara finial with brightly colored tiles. In front of the Minaret one can see the charming dome of the building.

Before the entrance of the building one can find a block of stone that dates from the Pharaonic period. On the left side of the entrance stands the mausoleum of Shaykh Amin El-Baghdadi that is placed behind a beautiful Mashrabiya screen. The interior plan of the Khanqah is designed in the military architecture style since the entrance does not lead directly to the main plan of the building. From inside the place consists of a central courtyard surrounded by four aisles. On either sides of a two-story height aisles by the end of the courtyard one can see the lodgings that were dedicated to the residence of a huge number of Sufis and Mamluk troopers and infants.