The mosque was demolished in 1993 at the order of the authorities of Republika Srpska as a part of an ethnic cleansing campaign,[2] and was rebuilt and opened on 7 May 2016.

[3][4] Commissioned by the Bosnian Sanjak-bey Ferhad Pasha Sokolović, the mosque was built in 1579[5] with money that, as tradition has it,[6] were paid by the Auersperg family for the severed head of the Habsburg general Herbard VIII von Auersperg and the ransom for the general's son after a battle at the Croatian border in 1575, where Ferhad Pasha was triumphant.

Above the stone basin was a decorative wrought iron trellis, and in the 19th century a wooden baldaquin and dome and painted attic in the so-called Turkish baroque style was added which was demolished in 1955.

According to legend, when the mosque was completed in 1579, Ferhad Pasha had the masons locked inside this minaret, sentencing them to death so they could never make anything so beautiful, but one night they made wings and flew away.

[12] Several weeks after the destruction of Ferhadija the nearby Sahat Kula, one of the oldest Ottoman clock towers in Europe, was also destroyed.

At the International Criminal Tribunal for the former Yugoslavia, a Serb leader from Banja Luka, Radoslav Brđanin, was convicted for his part in organizing the destruction of Muslim property including mosques, and also in the ethnic cleansing of non-Serbs.

The New York Times reported that about 1,000 Orthodox Christian Serbs participated in the attack and threw rocks and burned vehicles, a bakery, Muslim prayer rugs, and the flag on the Islamic center, where they hoisted the Bosnian Serb flag; drove a pig onto the site of the mosque as an insult to Muslims; and trapped 250 people in the Islamic center including the head of the UN in Bosnia, the ambassadors from Great Britain, Sweden and Pakistan, and other international and local officials.

[16] However, this ruling was subsequently overturned by the highest court in Sarajevo when the Serb Republic objected to paying for the damage caused by individual people.

The Regional Plan for Bosnia and Herzegovina to 2002 listed the Ferhat Pasha Mosque in Banja Luka as a Category I building under serial no.

[4] Notes: 1The ICTY Trial Chamber is satisfied beyond reasonable doubt both that the expulsions and forcible removals were systematic throughout the Autonomous Region of Krajina (ARK), in which and from where tens of thousands of Bosniaks and Bosnian Croats were permanently displaced, and that this mass forcible displacement was intended to ensure the ethnic cleansing of the region.

Bosniaks and Bosnian Croats were subjected to movement restrictions, as well as to perilous living conditions; they were required to pledge their loyalty to the Serb authorities and in at least one case, to wear white armbands.

The ICTY Trial Chamber is of the view that although this Agency was set up for the exchange of flats and the resettlement of populations, this was nothing else but an integral part of the ethnic cleansing plan.