The Thrashers were interested in Stewart going into the 2001 draft, but did not select him. Later that year he was signed as a free agent, after playing for the team as an invitee in the 2001 Traverse City Tournament.
Voted as the OHL’s top penalty killer for 2001-02 by the league’s coaches. Second among vote-getters for Fastest Skater and Hardest Worker awards in annual OHL coaches’ poll for 2001-02.
Attended Thrashers 2002 and 2003 Prospect Camp, and was mediocre, but played well in the Thrashers 2002 Training Camp. Was the last cut from the Thrashers in October 2003, his first pro season.
Played with the Chicago Wolves of the AHL for most of the 2003-04 season. Called up for a few games to the Thrashers as well. Stewart spent the 2004-05 and 2005-06 seasons again with the Wolves and got called up in 2006.