Trajanovski made his debut for Australia in 1996 against Kenya in Pretoria. Despite scoring in only three full international matches for the "Socceroos", each time he scored a hat-trick. The first hat-trick was in the first leg of the 1996 OFC Nations Cup final against Tahiti in Papeete when he scored four of Australia's six goals. In the second leg of the final in Canberra he scored three goals to lead Australia to an 11–0 aggregate win. His third hat-trick was almost two years later in September 1998. Playing against Cook Islands he scored three or four goals as a substitute in Australia's 16–0 win.