Kovačić appeared for the Croatian national team at various youth levels, debuting in May 2008 in an under-14 friendly match against Slovakia.
Since 2011, he was a regular member of the Croatia under-19 and under-21 teams.
In August 2012, Kovačić received his first competitive call-up for the Croatian senior team match against Switzerland, but did not play because of injury.
Subsequently, he received a call up for 2014 FIFA World Cup qualification matches in March 2013.
He made his senior debut in a qualification match against Serbia on 22 March 2013, playing as a central midfielder alongside Luka Modrić, instead of a regular team starter, Ognjen Vukojević.
Four days later, he played against Wales at Liberty Stadium, coming on as a second-half substitute in a 1–2 win.
His third match of the campaign came in June, when Croatia faced Scotland in Zagreb and suffered a frustrating defeat as they were unable to score despite a string of good chances.
By the end of the qualifiers, Kovačić made two more competitive appearances for Croatia, as Croatia scraped into the FIFA World Cup play-offs having taken only one point from their last four qualifiers.
Although he didn't participate in the scoreless first leg of the play-off against Iceland in Reykjavík, Kovačić started the second and decisive leg between the two national teams in Zagreb, making an assist for the team's second goal as they reached the 2014 FIFA World Cup finals 2–0 on aggregate.

On 2 June 2014, Kovačić was confirmed as a member of Croatia's 2014 FIFA World Cup squad.
He was in Croatia's starting team for the opening game of the tournament, a 3–1 defeat to World Cup hosts Brazil at the Arena Corinthians, São Paulo, where he played for his team for 60 minutes before being substituted.
He went to play all the remaining games in the group stage, as Croatia was eliminated in a group stage.
On 7 June 2015, he scored his first international goal in a 4–0 victory over Gibraltar, coming in his 20th appearance for the team.

On 4 June 2018, Kovačić was selected in Croatia's 23-man squad for the 2018 FIFA World Cup.
On 22 June, Kovačić provided an assist to his teammate Ivan Rakitić as he scored Croatia's third goal in a 3–0 win over Argentina in their second group stage match of the tournament.
Croatia was beaten 4–2 by France in the final on 15 July.

Kovačić appeared in Croatia's Nations League matches against Spain away and England home, that ended up as 6–0 defeat and a goalless draw, respectively.
He featured throughout Croatia's successful Euro 2020 qualifying campaign, as they finished top of the group.
In a 2–1 win over Wales in Osijek on 8 June 2019, he scored what would have been a goal for 2–0, however it was disallowed as Andrej Kramarić was in an offside position.
In a return leg on 13 October, in the build-up to the Wales goal, Kovačić was controversially injured by Ben Davies as the match ended up as a 1–1 draw.
Kovačić appeared for the Croatian national team at various youth levels, debuting in May 2008 in an under-14 friendly match against Slovakia. Since 2011, he was a regular member of the Croatia under-19 and under-21 teams. In August 2012, Kovačić received his first competitive call-up for the Croatian senior team match against Switzerland, but did not play because of injury. Subsequently, he received a call up for 2014 FIFA World Cup qualification matches in March 2013. He made his senior debut in a qualification match against Serbia on 22 March 2013, playing as a central midfielder alongside Luka Modrić, instead of a regular team starter, Ognjen Vukojević. Four days later, he played against Wales at Liberty Stadium, coming on as a second-half substitute in a 1–2 win. His third match of the campaign came in June, when Croatia faced Scotland in Zagreb and suffered a frustrating defeat as they were unable to score despite a string of good chances. By the end of the qualifiers, Kovačić made two more competitive appearances for Croatia, as Croatia scraped into the FIFA World Cup play-offs having taken only one point from their last four qualifiers. Although he didn't participate in the scoreless first leg of the play-off against Iceland in Reykjavík, Kovačić started the second and decisive leg between the two national teams in Zagreb, making an assist for the team's second goal as they reached the 2014 FIFA World Cup finals 2–0 on aggregate.
On 2 June 2014, Kovačić was confirmed as a member of Croatia's 2014 FIFA World Cup squad. He was in Croatia's starting team for the opening game of the tournament, a 3–1 defeat to World Cup hosts Brazil at the Arena Corinthians, São Paulo, where he played for his team for 60 minutes before being substituted. He went to play all the remaining games in the group stage, as Croatia was eliminated in a group stage. On 7 June 2015, he scored his first international goal in a 4–0 victory over Gibraltar, coming in his 20th appearance for the team.
On 4 June 2018, Kovačić was selected in Croatia's 23-man squad for the 2018 FIFA World Cup. On 22 June, Kovačić provided an assist to his teammate Ivan Rakitić as he scored Croatia's third goal in a 3–0 win over Argentina in their second group stage match of the tournament. Croatia was beaten 4–2 by France in the final on 15 July.
Kovačić appeared in Croatia's Nations League matches against Spain away and England home, that ended up as 6–0 defeat and a goalless draw, respectively. He featured throughout Croatia's successful Euro 2020 qualifying campaign, as they finished top of the group. In a 2–1 win over Wales in Osijek on 8 June 2019, he scored what would have been a goal for 2–0, however it was disallowed as Andrej Kramarić was in an offside position. In a return leg on 13 October, in the build-up to the Wales goal, Kovačić was controversially injured by Ben Davies as the match ended up as a 1–1 draw.
Mateo Kovačić