He was drafted by Essendon with the second selection in the 2006 AFL Draft. Prior to the Draft, Gumbleton was widely seen as one of the top key position players for his age group, and was expected to be Essendon's first pick in the number 2 spot. As a natural centre half-forward player, Gumbleton's imposing figure places him in the immediate spotlight, with North Melbourne recruiting manager Neville Stibbard already talking of an upcoming rivalry between Gumbleton and the third draft pick of the same year, Lachlan Hansen, who has been described as a natural centre half-back.
Gumbleton's 2007, 2008 and 2009 seasons were all plagued by injury and he played only five AFL games in first three seasons, all of which were in 2007. However, the 2010 season saw much improvement for Gumbleton, having a full pre-season, playing 17 of the first 18 games and being re-signed by Essendon, after showing much improvement. Gumbleton suffered yet another injury in round 18, with broken ribs and a punctured lung, ruling him out for the remainder of the 2010 season. Scott's 2011 season was again plagued by injury and he failed to play any games at AFL level. At the end of 2011 Scott had back surgery to repair a disk in his. It was hoped the surgery would fix his chronic hamstring issues. In 2012 Scott played his first senior game in nearly two years when he returned against Port Adelaide in round 16, booting three goals. He finished the 2012 season having played six games kicking 11 goals. Despite having long-term offers from rival clubs at the end of 2012 Gumbleton showed his loyalty to Essendon agreeing to a new one-year deal to remain at the club until at least the end of 2013.