He got his first head coaching job at S.C. Salgueiros in 1988 and stayed with the club for five seasons. He orchestrated the club's most notable moments in history by becoming Second League champion in 1989–90 and achieving UEFA Cup participation through best placement in club's history immediately in the next season. In 1993, he moved to S.C. Beira-Mar where he coached for a season. In 1994, he returned to S.L. Benfica for a two-year spell where he was the assistant coach and interim head coach winning one Portuguese Cup in 1996, and participating in the UEFA Champions League. During 1997 he coached Boavista. From mid-1990s Zoran Filipović was on the FR Yugoslavia national team coaching staff as an assistant to head coach Slobodan Santrač. He was part of Yugoslav coaching staff at the World Cup 1998, leaving the post together with Santrač right after the tournament. After joining as their head coach for a short spell, he left to work as part of Sampdoria coaching staff. Vujadin Boškov called him on to become his assistant during the second part of the 1998 season. Zoran Filipović's next stop was Vitória S.C. in the Portuguese league. However, Zoran Filipović re-joined the FR Yugoslavianational team in 1999 continuing his collaboration with Vujadin Boškov when he took over. Filipović was the assistant at the Euro 2000. Following Euro 2000, he briefly coached Panionios in Greece. In 2001 Zoran Filipović returned to coach Red Star Belgrade in Serbia until 2003 with which he won the 2001–02 FR Yugoslavia Cup title and is remembered for launching young players such as Nemanja Vidić, Boško Janković, Nikola Žigić, Aleksandar Luković amongst others. In 2003 Zoran Filipović went to the United Arab Emirates when coaching Al-Shaab with which he was defeated in the Cup finals. After the Emirates experience, he became the technical director of the Football Association of Serbia and Montenegro A and u21 squads participating in the 2006 FIFA World Cup in Germany and the 2006 U21 European Championship in Portugal. On 1 February 2007 he was appointed the first coach of the newly created Montenegro national team. His first game in charge was a friendly against Hungary on 24 March 2007 where they won their debut match with 2–1. The record in the newly formed Montenegro national team was more than positive for a team rated always as underdogs – of a total of 23 matches played, 8 victories were achieved, 8 draws and 7 defeats. The FA president Dejan Savićević commented when Zoran Filipović's contract expired in January 2010 – "Filipović did an enormously good job. He formed a great group of players and worked with great enthusiasm." Zoran Filipović left the Balkan newcomers in an astonishing 73rd position in the FIFA ranking when he departed from this historical role. Only two months after leaving the helm of Montenegro national team he assumed a 3-month coaching job contract in Romanian club FC Ceahlăul Piatra Neamţ. In July 2010 he was hired by South African club Golden Arrows from Durban. With only three months left in the championship and with relegation imminent, Zoran Filipović arrived in FC Atyrau to save the team from relegation. He stayed on to sign a one-year contract for season 2012. In May 2016 it was announced by Serbia that Zoran Filipović will return to national team football in a new role.
Zoran Filipović still has the goal record in European competitions for Red Star Belgrade – 28 goals. Zoran Filipović is ranked the 3º Top goalscorer for Red Star – 502 games/302 goals. Zoran Filipović in season 1982–83 he contributed to Benfica's European good campaign – 12 games/8 goals.
