He then went on to coach Marsonia, with which he earned a promotion to the Prva HNL. He took over Osijek in 2003, his first club as a professional football player, finishing again on the 4th place in the competition and reaching the quarter-finals of the Croatian Cup. In 2010 he once again became the coach of Osijek. After accepting an offer from Slaven Belupo in 2004, he managed to finish on the 6th place and qualified for the Intertoto Cup where the club played against Deportivo La Coruña. This was the first international appearance in his career as the coach. During the 2005–06 he managed the team of Cibalia finishing on the 9th place in Prva HNL. After a 1-year absence of coaching, he accepted the project Slavonac CO, which he managed from 2007 to 2009. With the club he made a historic result qualifying for the Prva HNL, although they have never played in it due to financial reasons. When he took over Šibenik in the 2009–10 season, he managed to put down the best result in the club's history finishing on the 4th place in domestic competition and playing the final of the Croatian Cup against Hajduk Split. They qualified for the UEFA Europa League, where they successfully passed the 1st round of qualifications. They then played against Cyprian powerhouse Anorthosis Famagusta FC. In 2011 he became the head coach of Široki Brijeg in the Bosnian Premier League. There, he also reached the final of the Bosnian Cup and finished as runner-ups in the competition. In the 2013–14 season he achieved his best result yet as a manager, when he won Bosnian Premier League with Zrinjski Mostar, although they were considered underdogs throughout the whole season. They earned the right to play in the UEFA Champions League where they played against NK Maribor. At the end of year 2014, Karačić was sacked. During the 2015–16 season he managed NK Vitez, and during late 2016 he managed NK Široki Brijeg. On 4 October 2017 he was named as the head coach of Vitez for the second time. In October 2018, Karačić became the new manager of Varaždin. On 18 May 2019, he got Varaždin promoted to the Prva HNL after the club beat Šibenik 3–1 at home.