[7] In October 2001, Kek returned to Maribor as an interim manager after Ivo Šušak resigned.

[1] On 5 January 2007, Kek was appointed manager of the Slovenia national team,[12] which he led to the 2010 FIFA World Cup after beating Russia in the play-off.

On 24 October 2011, after the unsuccessful UEFA Euro 2012 qualifications, Kek and the Football Association of Slovenia came to a mutual agreement on the early termination of his contract.

[15][16] On 27 February 2013, after more than a year without contract, Kek took over Croatian top division club HNK Rijeka.

[21] On 7 September 2017, Kek became the longest-serving manager by single appointment in the history of the Croatian First Football League.

[24] He managed the team in the UEFA Euro 2020 qualifiers, where Slovenia finished in fourth place with four wins out of ten games.

[26] In the UEFA Euro 2024 qualifiers, Kek guided Slovenia to second place in the group after defeating Kazakhstan 2–1 on the final matchday, securing the country's first European Championship appearance in 24 years.

[27] Matjaž's father, Franc, played for NK Maribor during the early 1960s, earning 51 appearances for the club and scoring one goal.