Ivanković then became an assistant manager to Miroslav Blažević, who led the Croatia national team to a sensational third-place finish at the 1998 World Cup finals in France.

[5] 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.

[6] 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).

The Iranians managed to equalise fifteen minutes later, eventually scoring their only point at the 2006 World Cup since the match ended in a 1–1 draw.

After the World Cup, MPE removed the Head of the Football Federation of Iran, replacing Ivanković with Amir Qalenoei.

[8] On 6 November 2006, Ivanković replaced Josip Kuže as the head coach of Croatian club Dinamo Zagreb.

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.

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.

[21][22] 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.

[23] Under Ivanković, Oman pulled off a historic win over Japan in the final round of the 2022 FIFA World Cup qualifiers.

[26] On 24 February 2024, Ivanković was announced as the head coach of China national football team, replacing former Yugoslav compatriot Aleksandar Janković.