Henderson played his junior football in Birregurra, Victoria, before entering the AIS-AFL Academy, from which he graduated in 2007, the same year he completed his schooling at The Geelong College.

Henderson made his debut for Carlton in Round 1, 2010 against Richmond, and he kicked three goals in the Blues' second-round game against his old team.

However, Henderson was sufficiently impressive in the role that he held his place as a key defender, either full-back or centre half-back, for the rest of the season.

[3] Under new coach Mick Malthouse coming in to replace former coach Brett Ratten for the 2013 AFL Home and Away season, Henderson started the season as a backman and showed promising signs, keeping the West Coast Eagles' Josh Kennedy goalless in Round 4.

At the end of the 2013 Toyota AFL season, Henderson finished 3rd in Carlton's best in fairest (John Nicholls Medal), after winner Kade Simpson and Andrew Walker.