He grew up in Calgary, Alberta, Isbister played junior hockey with the Calgary Canucks of the Alberta Junior Hockey League, recording 49 points in 35 games in 1992–93. The following season, he began his career in the Western Hockey League with the Portland Winter Hawks. After a 16-goal, 36-point season in 1994–95, he was drafted in the third round, 67th overall, by the Winnipeg Jets in the 1995 NHL Entry Draft. Upon being drafted, he returned to the Winter Hawks and recorded 89 points, as well as a team-high 45 goals. In his final year with the Winter Hawks, Isbister recorded 33 points in 24 games and was named to the WHL West Second All-Star Team. That season, he also competed for the Team Canada at the 1997 World Junior Championships and made his professional debut with the Springfield Falcons of the AHL, appearing in 7 games.