He played for a variety of sides in two stints in the National Soccer League. The first stint was played almost entirely for Sydney United, for whom he played as a junior, and which culminated in playing in their runner-up 1996/97 side. After that season he moved to NAC Breda in the Netherlands, and after 2 seasons there went to Croatia's NK Rijeka, where he was the club's top scorer in 2000/01 with 10 goals. On his return to the NSL in season 2001/02, he rejoined Sydney United for a brief stay, before moving to city rival Sydney Olympic during the same season. He would spend the rest of the season and the next playing there, including scoring the only goal of the 2001/02 Grand Final against Perth Glory. In the final he was awarded the Joe Marston Medal, delivering Sydney Olympic their second NSL title, as well as playing in the runner up side the following season against Perth Glory.
In the 2003–04 season, the NSL's last, Miličić moved, this time to Parramatta Power, where he would again experience Grand Final defeat against the Perth Glory. After the NSL was disbanded, Miličić played in the Malaysian League for Pahang. It was widely felt that with the $1.5 million salary caps imposed on all Hyundai A-League clubs, Miličić would not be able to be brought back to Australia. However, he joined the Newcastle United Jets, who finished 4th on the Hyundai A-League ladder in 2005/2006, also joining close friends Labinot Haliti, Ned Zelic.
Ante Miličić was the first player in the A-League to score a Hat-Trick in the game Newcastle Jets vs New Zealand Knights on 4 November 2005 in round 11. In May 2006 Ante signed to transfer to rival A-League team Queensland Roar, where he played in 44 matches scoring 11 goals. On 8 December 2007, Miličić had his contract terminated by mutual consent and joining Malaysian Premier League Shahzan Muda FC, citing that "It wasn't quite happening for me at Queensland Roar."
Miličić returned home to his club, Sydney United as player/coach for season 2009 and 2010 in the NSW Premier League. It is his first venture as coach and currently boasts a record of 9 wins (8 in Premier League 1 Tiger Turf Cup), 2 Draws and 1 Loss.
He was also called up as an assistant coach to the Under 20's Young Socceroos team for the 2009 FIFA U-20 World Cup in Egypt and Assistant in Under 20s World Cup in Colombia 2011.
On 18 November 2009 it was announced that he would be joining Jesper Olsen as an assistant coach at new A-League franchise Melbourne Heart.
After being passed over for the vacant manager position at Melbourne Heart, he joined his close friend Tony Popovic as the inaugural assistant coach of Western Sydney Wanderers FC.
At the end of the 2013/14 A-League season, Milicic joined Ange Postecoglou as assistant coach of the Socceroos, Australia's national football team.
With Australia:OFC Nations Cup: 2004
With Sydney Olympic:NSL Championship: 2001–2002
With Trinity Grammar 4th XI:Cassen Cup- Most Ouststanding Opens Team: 2009
Personal Honours:Joe Marston Medal: 2001–2002 with Sydney Olympic
Johnny Warren Medal: 2003–2004 with Parramatta Power
NSL Top Scorer: 2003–2004 with Parramatta Power – 20 goals