MacKenzie began his junior career playing for his hometown Sudbury Wolves of the Ontario Hockey League (OHL). Following his second season, in which he increased his point production from 20 to 87, he was drafted by the Atlanta Thrashers in the fifth round, 128 overall, in the 1999 National Hockey League (NHL) entry draft. In his final season, he registered 40 goals and 89 points leading the Wolves in points and finishing sixth in the OHL. He also finished with a face-off winning percent of 67%, winning both the OHL and Canadian Hockey League (CHL) Face-off Awards.