Chartier played junior hockey in the Western Hockey League (WHL) for the Saskatoon Blades and Prince George Cougars. Chartier was drafted 199th overall in the 1999 National Hockey League (NHL) Entry Draft by the Edmonton Oilers. During his final season in the WHL (2000-01), Chartier was awarded the Bill Hunter Trophy as the WHL's Top Defenceman. While playing in Prince George, Chartier spent much of his time paired with Dan Hamhuis of the Vancouver Canucks. After the 2000-01 season, Chartier and Hamhuis were both named to the WHL's First All-Star Team.