Ivanković also led Iran to qualify for the 2006 World Cup, the third time in the country’s history (they had previously been eliminated in the first round in 1978 and 1998).

Ivanković was appointed to the head of the Iranian team on 29 January 2002. Under Ivanković, Iran’s U23 football team won the 2002 Asian Games in Pusan. He remained the coach of the national team until the end of 2002, when he was replaced by Homayun Shahrokhi.

Ivanković had become very popular in Iran and the public media demanded a contract renewal, but the Football Federation was initially reluctant to appoint him as the head coach. Finally after a period of negotiations he was reappointed as the head coach of Iran on 3 October 2003.

On 6 November 2006, Ivanković replaced Josip Kuže as the head coach of Croatian club Dinamo Zagreb. He led the club to the Double in 2007 without losing a single competitive match. On 14 January 2008, he resigned as the coach of Dinamo Zagreb, mostly due to his differences with the club’s executive vice-president Zdravko Mamić.

Ivanković returned as the manager of Dinamo Zagreb on 21 May 2008. He replaced Zvonimir Soldo, who resigned immediately after Dinamo won the domestic double.

In July 2009, Ivanković was offered the role of Persepolis manager in Iran, but he rejected the offer.

On 17 December 2009, Ivanković was appointed as the new head coach of Chinese giant Shandong Luneng. In his first season, he led the team to the 2010 Chinese Super League winners with a record 63 points. The team secured the qualification for 2011 AFC Champions League, but Shandong were eliminated in the first round with 7 points. Due to poor result in the Champions League, he was dismissed on 10 May 2011, seven days before crucial game with Cerezo Osaka, which they lost by a score of 0–4.

On 22 July 2011, Ivanković signed a one-year contract with Ettifaq to lead the club in the 2011–12 Saudi Professional League and return club to the AFC Champions League. He was sacked on 29 April 2012 after finishing the 2011–12 season in fourth.

In May 2012, UAE Pro-League side Al-Wahda said it signed a two-year contract with Ivanković and that he would take charge at the club in the 2012–13 season, but his contract was terminated on 27 April 2013, after a 3–4 loss to Ajman Club. At the time of his dismissal, Al Wahda was ranked at the 7th place.

On 2 September 2013, Ivanković returned to Dinamo Zagreb, the club he led from 2006 to 2008. However, he was sacked on 21 October 2013, after just five games.

On 5 April 2015, Ivanković was confirmed as the new manager of Persepolis, signing a 1½-year contract with the club. After good performances with the club, which left the team in the first place with six matches remaining, Ivanković extended his contract with Persepolis in April 2016 to the end of the 2017–18 season and in 2017 to the end of the 2019–20 season. After the end of the 2018–19 season, it was reported that he was signed for Ahli Jeddah before returning to Croatia for his annual vacation. Ivanković announced that he will leave Persepolis on 11 June 2019.

On 18 June 2019, he was confirmed signing a two-year contract with Al-Ahli. On 16 September 2019, he was officially sacked after just five games due to poor results.

On 19 January 2020, Ivanković was announced as the head coach of the Oman national team to succeed Erwin Koeman after the latter’s dismissal.