The Gazi Husrev bey khaniqah was buil by the end of 1531. In addition to the performance of Sufi worship and dhikr, it was also used to provide dervishes with the necessary knowledge of the internal meanings of Islam.
The Gazi Husrev bey khaniqah was damaged on several occasions, but the last of which was in 1931, when the new madrassa building was erected. It was reconstructed in 1998.
Aside of dervish way of worship and dhikr, here dervishes were able to acquire all the necessary knowledge at the end of Khaniqah madrassa, were able to go all across Bosnia and Herzegovina to the mission of transferring the Sufi doctrine.

The head of Khaniqah, according to the vakufnama, was Sheikh of Halvati order.
Motifs which guided Gazi Husrev bey that the head of this Khaniqah would be dervish from this order, should be sought in the fact that this mystical school, to which he belonged, and which was very widespread in Anatolia and Rumelia at his time, and because this order was very consistant and strict in rearing dervishes, and had greatly respected leaders of the government.
Later, however, some major representatives of this order came into conflict with Ottoman authorities, which was one of the reasons why the head of this Khaniqah was given to representative of Naqshabandi order in the beginning of the 20th century, whom to belonged his successors.
In addition, we can assume that in that time there was not capable Shaikh of Halveti order, and were resorted to another solution.
Gazi Husrev beys Khaniqah was very often destroyed, so in records there are sufferings during the invasion of Eugone of Savoy in 1697, according to Mula Mustafa Bašeskija it was burnt in 1755/6. In 1779 it was repaired, but again in 1831 because a large fire, which destroyed almost whole Gazi Husrev beys foundation, Khaniqah was damaged again.
During the Austria-Hungarina rula it was quite destroyed but renewed, and during the 1931 while the new building of Gazi Husrev beys Madrassa a large part of this building was destroyed.
The reconstruction was completed in 1998.