After a fine junior career in the QMJHL that lasted three seasons with stops in Sherbrooke, Moncton and Laval, Aubin joined the Pittsburgh organization, which had drafted him 76th overall in 1995.
He spent 1997-98 in the minors, before getting his first NHL opportunity the following year, appearing in 17 games. He recorded two shutouts and had an excellent 2.22 goals against average, showing skills that led the Penguins to believe he could one day inherit the starter's job which then belonged to Tom Barrasso.
The next season, Aubin did, in fact, take the number one role, playing 51 games, and leading the NHL for rookie goalies with 23 wins. He also became only the second Pittsburgh goalie to win more than 20, a feat he repeated in 2000-01.
Over the next two years, Aubin would battle injuries and would see limited action after the Penguins had acquired Johan Hedberg from the San Jose Sharks towards the end of the 2000-01 season and was eventually assigned to the Penguins AHL affiliate in Wilkes/Barre Scranton.
With the Penguins, Aubin split his time between the parent club and Wilkes-Barre/Scranton before signing with the Toronto Maple Leafs in the summer of 2005. Aubin spent most of his time with the Maple Leafs' AHL affiliate that year but was called up during the latter half of the season for the Leafs. In his eleven starts that season with the Leafs, Aubin went 9-0-2 and single handedly almost led the Leafs into the playoffs. After appearing in 20 games as a back-up with the club in 2006-07, he was signed as an unrestricted free agent on August 28, 2007 by the Los Angeles Kings. Aubin started in 12 games with his new club in 2007-08 and posted a 5-6-1 record on a Kings team that struggled to stay out of the Western Conference basement. He was subsequently dealt to the Kings rival in Anaheim at the NHL trading deadline on February 26, 2008 for a 7th round draft pick in 2008.