2009-10: Troy Bourke made his WHL debut, appearing in five games with the Prince George Cougars, and was the leading scorer for the St. Albert Sports Raiders in the Alberta Midget AAA Hockey League. Bourke joined the Cougars, who would finish with the WHL's worst record, at the end of February and scored 3 goals while finishing minus-one with 4 penalty minutes. In 34 games with the Raiders he scored 27 goals with 26 assists and had 24 penalty minutes. In the Raiders' five-game playoff series with Leduc he scored 2 goals and had 4 penalty minutes.
2010-11: Bourke skated in 68 games for a much-improved Prince George squad and represented Canada Pacific in the 2011 U17 World Hockey Challenge. In 68 games for the Cougars he scored 19 goals with 23 assists and was plus-15 with 20 penalty minutes. Prince George reached the playoffs after finishing fourth in the B.C. Division. In four playoff games Bourke had 1 assist and was minus-four. Bourke was the third-leading scorer for Canada Pacific, which won a bronze medal at the WHC. In six games he scored 3 goals with 5 assists and had 14 penalty minutes.
2011-12: Bourke was the leading scorer for Prince George and represented Canada in the 2012 U18 World Junior Championship. In 71 games he scored 18 goals with 38 assists and was minus-12 with 56 penalty minutes, including three fighting majors. Prince George missed the WHL playoffs, finishing last in the B.C. Division. Bourke shared the assists lead for Team Canada at the WJC with defenseman Mathew Dumba, finishing with seven and was plus-seven in seven games. Canada defeated Finland in the bronze medal game. Bourke was ranked 123rd amongst North American skaters in Central Scouting's final rankings and was selected by Colorado in the third round (72nd overall) of the 2012 NHL Draft.
2012-13: Bourke was the second-leading scorer for Prince George in his third season with the Cougars. He scored 15 goals with 35 assists and was -30 with 37 penalty minutes. The season was a frustrating one in Prince George — the Cougars finished with the WHL's second-worst record and changed coaches in mid-season.