He is currently the head coach of the Brisbane Lions in the Australian Football League (AFL), where he won the premiership in 2024.

[5] On 4 October 2016, Fagan was appointed as the senior coach of the Brisbane Lions, replacing Justin Leppitsch.

[8] On 1 March 2023, the Brisbane Lions announced that Fagan had signed a contract extension that would keep him at the club until the 2025 season.

[9][10] In the 2024 season, after staging the second highest finals comeback against Greater Western Sydney in the semi-final, coming back from 44 points down.

Fagan coached the Brisbane Lions to the 2024 Grand Final, where they defeated Sydney Swans by 60 points to win the premiership.