Leko made his debut as a manager in 2014, with
OH Leuven. In 2015, he became an assistant manager of Greek side
PAOK under the coaching staff of Croatian manager
Igor Tudor, who was sacked in 2016. For the 2016–17 season, he managed
Sint-Truiden; for the next two seasons, 2017–18 and 2018–19, Leko was the manager of
Club Brugge. He celebrated
Jupiler Pro League and
Belgian Super Cup in his first season in Brugge. Also, Leko won the title of
Professional Manager of the Year. In October 2018, Belgian police interrogated him for corruption investigation. In May 2019,
Club Brugge and Leko parted ways. The 41-year-old coach had been with the club since 2017. On 1 June 2019, he was appointed at his new club,
Al Ain. In December 2019, Leko left club
Al Ain after a disastrous home defeat against
Al Dhafra. Both sides had agreed to end their cooperation after five months of poor play. On 20 May 2020, Leko was appointed the manager of
Royal Antwerp. Taking over the team from
Laszlo Bölöni, he led the team to win their first
Belgian Cup since 1992, with a 1–0 win against his former side Club Brugge in the final. This earned Antwerp a qualification in the
2020–21 UEFA Europa League group stage for the first time in the club's history, where they were drawn in Group J against
Tottenham Hotspur,
LASK Linz and
Ludogorets Razgrad. Leko led the team to a surprising second place finish in the group, with four wins and two losses, culminating in a 1–0 home victory against Tottenham on 29 October; as a result, the team qualified for the round of 32, where they were drawn against
Rangers. In December 2020, Leko left Royal Antwerp and moved to
Shanghai Port, where he took up his new post with the Chinese team, under a two-year contract worth five million euros. In February 2021, Leko was introduced as the new head coach of Shanghai Port at the
SAIC Motor Pudong Arena. On 31 December 2022, he returned to Croatia to coach his former club Hajduk Split; however, he was dismissed on 23 October 2023. On 4 January 2024, he became head coach of Belgian side
Standard Liège. On 4 June 2025, Ivan Leko was officially appointed manager of Belgian
Pro League side
KAA Gent. On 8 December 2025, Leko returned to
Club Brugge. ==Investigation==