Mijatović was an assistant coach at Cibona Zagreb from 2001 to 2003.[2] During the 2002–03 season, he temporarily replaced the suspended Aleksandar Petrović as head coach.[3] In 2007, Mijatović again became an assistant coach at Cibona.[4] When Cibona's head coach Velimir Perasović moved to Anadolu Efes in Turkey in 2010, Mijatović was considered as his successor at Cibona.[2] However, Mijatović followed Perasović to Anadolu Efes.[5] As an assistant coach, Mijatović won the EuroLeague with the team in 2021 and 2022 and was also crowned Turkish champion and cup winner three times each. He worked in Istanbul under Ergin Ataman and Dušan Ivković, among others.[6]
In February 2024, Mijatović was promoted to head coach of Anadolu Efes.[7] In his first season as head coach, the club won the 2023–24 Basketbol Süper Ligi regular season,[8] but fell short to Fenerbahçe in the finals.