In the winter of 2000, he left Brotnjo and became an assistant manager to Mišo Smajlović in the Bosnia and Herzegovina national team. Slišković became the head coach of the national team in March 2002, after Smajlović left the team because of his contract expiring. Slišković stayed as the head coach until 2006. In 2004, he won the award "Best Bosnia and Herzegovina Coach" by Dnevni Avaz and the "Bosnia and Herzegovina Man of the Year" also in 2004. While Bosnia and Herzegovina head coach, in October 2004, Slišković replaced Ivan Katalinić and simultaneously became the new Hajduk Split manager. In his only season as Hajduk's manager, Slišković won the 1. HNL with the club in the 2004–05 season.