Lyons was drafted with selection 61 in the 2010 AFL draft by, having previously played for the Sandringham Dragons in the TAC Cup. He did not play in his first AFL season, but showed good signs with South Australian National Football League side,. Lyons made his AFL debut in round 5 of the 2012 season, against at AAMI Stadium in Showdown XXXII. He played only three games in that season but continued to perform in the SANFL and could have played more if it hadn't been for an ill-timed foot injury. Lyons played nine games in 2013, including a 21-disposal game against in round 9 and a four-goal effort against in round 16. At the end of the season he ignored considerable interest from, where his father Marty had played, to stay with the Crows. Lyons played ten games in 2014, beginning to cement his place in the side in the latter half of the year. Despite again attracting interest in the trading period, Lyons rebuffed all other offers to sign with the Crows for another two years. In late 2014 Lyons was bitten on the leg while asleep and developed symptoms consistent with a white-tailed spider bite, leading to him being hospitalised. He recovered to play 13 games for the 2015 season, nine of them as Adelaide's starting substitute, in what was a trying year for the club, following the mid-season murder of their coach, Phil Walsh. Lyons had his best season at the Crows in 2016, playing 20 games, kicking 15 goals and averaging 22 disposals, in his first season under new coach Don Pyke.
At the conclusion of the 2016 season, Lyons was traded to. Lyons slotted straight into the midfield at the Suns and enjoyed a career-best season in 2017, playing 18 games and averaging 25 disposals, despite the Suns only winning six games and their coach, Rodney Eade, being sacked towards the end of the season. Lyons played 19 games in 2018 and again averaged 25 disposals, and was also equal-third in the AFL for clearances. Despite this, new coach Stuart Dew dropped him twice during the season, and he was delisted at the end of the season with a year left on his three-year contract.
Brisbane Lions (2019–present)
Lyons was signed by the at the beginning of the 2018 first delisted free agency period on 1 November 2018, the day after his delisting from Gold Coast, joining his younger brother Corey at the club. He made his debut for the club in a 44-point upset win against reigning premiers at the Gabba in round 1 of the 2019 season, and played his 100th career game in the loss to the at Mars Stadium in round 8. After accumulating 33 disposals and eight marks in a best-on-ground performance in the win against at the Gabba in round 11, Lyons had a career-best game in the win against Port Adelaide at Adelaide Oval in round 17, accumulating 36 disposals and nine tackles, and followed up a week later against North Melbourne with 30 disposals and two goals. He went on to poll a career-high 13 votes in the Brownlow Medal and finished fourth in voting for the Merrett–Murray Medal, in what was a career-best season.
