Stoll started his Western Hockey League (WHL) career at the end of the 1997–98 season with the Ice, while they were still located in Edmonton.
After this season, the team relocated to Cranbrook, British Columbia, and were renamed the Kootenay Ice.
He played his entire junior career with the Ice franchise.
In his third season, he was named team captain.
In his final junior season (2001–02), Stoll captained the Ice to a Memorial Cup championship.

While playing in Kootenay, Stoll went through the NHL draft process twice.
In his initial year of eligibility, he was selected by the Calgary Flames 46th overall in the 2000 NHL Entry Draft, but was unable to come to terms with the team.
The Flames arranged a trade to the Toronto Maple Leafs, who thought they had made arrangements to have a contract signed by the appropriate deadline, but their fax to NHL headquarters did not make it in time.
Stoll ended up re-entering the 2002 NHL Entry Draft, where he was selected by the Edmonton Oilers 36th overall.

Also during his junior career, Stoll twice represented his country at the World Junior Hockey Championships, in 2001 and 2002, winning bronze and silver medals respectively.
 In 2002, Stoll was named captain for Team Canada.
Stoll started his Western Hockey League (WHL) career at the end of the 1997–98 season with the Ice, while they were still located in Edmonton. After this season, the team relocated to Cranbrook, British Columbia, and were renamed the Kootenay Ice. He played his entire junior career with the Ice franchise. In his third season, he was named team captain. In his final junior season (2001–02), Stoll captained the Ice to a Memorial Cup championship.
While playing in Kootenay, Stoll went through the NHL draft process twice. In his initial year of eligibility, he was selected by the Calgary Flames 46th overall in the 2000 NHL Entry Draft, but was unable to come to terms with the team. The Flames arranged a trade to the Toronto Maple Leafs, who thought they had made arrangements to have a contract signed by the appropriate deadline, but their fax to NHL headquarters did not make it in time. Stoll ended up re-entering the 2002 NHL Entry Draft, where he was selected by the Edmonton Oilers 36th overall.
Also during his junior career, Stoll twice represented his country at the World Junior Hockey Championships, in 2001 and 2002, winning bronze and silver medals respectively.  In 2002, Stoll was named captain for Team Canada.
Jarret Stoll