Trajkovski died on 26 February 2004 in a plane crash en route to an economic conference in Mostar, Bosnia and Herzegovina. The aircraft crashed in thick fog and heavy rain on a mountainside in southeastern Herzegovina, near the villages of Poplat and Vrsnik some eight miles (15 km) south-south-east of Mostar. Eight other people were also aboard but none survived the impact, which broke the aircraft into three pieces. It came down in an area that had been heavily mined during the Bosnian War of the 1990s, which significantly hampered the rescue and recovery efforts.