At A.C. Milan, Šimić was immediately made a member of the first-team squad under Carlo Ancelotti, who changed Šimić's playing position from centre back to right back in a four-men defensive line. His debut for AC Milan came in a 2002–03 Champions League third qualifying round away game against Slovan Liberec on 28 August 2002. Šimić went on to make 12 appearances for AC Milan in their run to the UEFA Champions League title in 2003, though he was omitted from both semi-final legs against Inter and the final match against Serie A rivals Juventus at Old Trafford. He made 29 Serie A appearances for AC Milan in his first season with the club, but in the following three seasons he never regained his place as a first-team regular, making only 27 league appearances over the three seasons. In May 2006, he signed a contract extension until 2009 with AC Milan, just weeks after openly criticising coach Carlo Ancelotti over lack of playing time.