Zaharakis was selected by Essendon, the team he supported all his life, with their second (23rd overall) pick in the 2008 AFL Draft. He had previously been playing with the Northern Knights in the TAC Cup and was captain in 2008. He attended Our Lady Help of Christians (Eltham), finishing Year 12 in 2008 at Marcellin College where he also won the Terrence Cleary Memorial Sporting Award for sportsmanship and sporting excellence.
Zaharakis was awarded Essendon's number 11 guernsey which was previously worn by Damien Peverill and has been his number throughout most of his junior career. He kicked his first career goal for Essendon in the final seconds of the 2009 Anzac Day match to beat Collingwood by five points.
He played 10 games in his debut season and 20 in 2010. His 2011 season has been his most consistent and impressive season to date. He capped off the year by winning his first Crichton Medal as Essendon's best and fairest player.
At the 2013 Anzac Day match, in which Essendon defeated Collingwood by 46 points, Zaharakis won the Anzac Day Medal for best-on-ground performance. He had stats of 34 disposals, 14 contested possessions, 6 clearances, 6 Inside 50s and 4 goals.
It has been revealed by Zaharakis' manager that he did not take any part in Essendon's 2012 controversial sport science program that has since put the club under scrutiny by the AFL and ASADA (the Australian Sports Anti-Doping Authority) during the 2013 season.