At the very beginning of the Kosovo War, the unit was ordered to set up a temporary base of operations on the Goč mountain, near Kosovo. From there, JSO launched a number of operations aimed against the Kosovo Liberation Army. One of their first actions was the 1998 successful assault on the KLA commander Adem Jashari's hideout. Later in 1999, the unit engaged in a fierce battle in and around Peć. The unit operated a wide variety of armored vehicles, including American-made Hummers procured via Cyprus, which all proved to be effective for quick operations under constant NATO aerial bombardment. After the Kumanovo Agreement and the subsequent end of the war, the JSO, alongside the police and armed forces, left Kosovo.