Brampton Thunder win the first NWHL Championship Cup in 1998-99. After the Thunder have made it to the NWHL Championship Cup game three times, but has been defeated each time; first by the Beatrice Aeros in 2002, then by the Calgary Oval X-Treme in 2004, and finally by the Montreal Axion in 2006. They also played in the Esso Women's Nationals and were victorious in 2006, defeating the Montreal Axion to claim the national title.
The Thunder also have the distinction of having their home arena serve as the site of all NWHL Championship Cup games.
In 2007, the NWHL suspended operations. Players from the seven disbanded NWHL teams joined seven corresponding teams in the new Canadian Women's Hockey League. Players from the NWHL Brampton Thunder joined the CWHL Brampton Canadettes-Thunder. On January 18, 2011, the Thunder competed against the Montreal Stars at the Invista Centre in Kingston, Ontario. This is team captain Jayna Hefford’s hometown and she scored a goal in front of her closest friends, family and fans. In addition, her number 15 was raised to the rafters of the Invista Centre on behalf of the Kingston Area Minor Hockey Association. As of 2012, no sweaters bearing Hefford’s number will be used in Kingston Minor Hockey. On November 2, 2011, Jesse Scanzano was on loan from the Toronto Furies, as she appeared in one game for the Brampton Thunder. The game was an exhibition contest versus her alma mater, the Mercyhurst Lakers. In the second period of said contest, Scanzano scored the game-winning goal as the Thunder defeated the Lakers by a 3-1 tally.
In the championship game of the 2012 Clarkson Cup, Brampton fell to the Montreal Stars by a 4-2 tally. In the second period, Jayna Hefford found the puck alone in front of the Stars net, but was stopped by netminder Jenny Lavigne. In the third period, the Thunder were down by a 3-0 tally. Courtney Birchard started the scoring for Brampton (assisted by Vicki Bendus and Andrea Ironside) and with two minutes left in the game, Cherie Piper scored an unassisted goal to cut the lead to 4-2 (which would remain the final tally). Two Thunder players earned awards for their play in the Clarkson Cup. The Outstanding Defender award was given to Molly Engstrom, and netminder Liz Knox was given the Outstanding Goalkeeper award.