Aubin began his hockey career playing with the Rouyn-Noranda Huskies of the Quebec Major Junior Hockey League. In his rookie season of 2002-03, Aubin scored 14 goals and added 20 assists with the Huskies. In his next season, Aubin benefited from added ice time with the team, and recorded 29 goals for 65 points in 70 games. Aubin also recorded 116 penalty minutes on the year. In 2004-06, Aubin continued his growth as an offensive leader with the Huskies, as he finished the year tied as the team's leading scorer with 41 goals and 84 points. Aubin was also fifth in the league in goals, and second in game-winning goals with 10.
Aubin began the 2005-06 season with the Huskies, and scored 31 goals in 40 games with Rouyn-Noranda. However, midway through the season, Aubin was acquired by Quebec Ramparts' general manager Patrick Roy in a move to solidify the Ramparts' scoring. Aubin rewarded his new team with 32 goals and 78 points in 32 games while with the Ramparts. Aubin ended his split season with 57 goals and 117 points, which placed him sixth in the QMJHL in scoring. The Ramparts', and by extension Aubin's, success continued into the post-season, as the Ramparts went on to win the Memorial Cup as CHL champion.
In his final year of junior play, Aubin once again surpassed 50 goals on the season, scoring 51 in 68 games. He finished the season with 105 points, and contributed 8 points in a quick first round playoff exit for the Ramparts.
Aubin signed with the Toronto Marlies in 2006, and made his professional debut in the 2006-07 season, where he played 8 games for the Marlies, recording 2 assists. The following year, in his first complete season in the AHL, Aubin scored 10 goals and 22 points in 75 games, while adding 5 goals in 17 playoff games for the Marlies.