1996 the Peel Thunder Football Club and the WAFC negotiated the issue of the ninth licence in the WAFL competition to the Mandurah (Peel) region. The licence was issued on the proviso that the Club be ready to compete in the 1997 WAFL competition which left only eight months to establish the Club's administration and recruit coaches and players in order to field teams in time for the 1997 WAFL competition.
The 2008 season was a big one for Peel Thunder. The League side narrowly missed out on finals action while the "Pocket-Rocket" Hayden Ballantyne added a second Sandover Medal to the Club's name in a phenominal season-long performance. Coach Chris Waterman re-signed as Senior Coach of the club making him the longest serving coach the Thunder have had.
Despite its difficult and relatively short history Peel Thunder has achieved much with its Colts team becoming WAFL Colts Premiers in 2004 and 2005 and runners-up in 2006. The Reserves team also competed in the Grand Final in 2005.
The Club is now taking the approach of concentrating on developing players from within the Peel district rather than recruit from outside its zone – an approach which appears to be paying dividends.
In 2002 Alistair Pickett became the Club's inaugural Sandover Medallist with teammates Daniel Wells placed equal second and Darren Bolton in fourth place.
In recent years the Club has proved fertile ground for recruitment of young AFL players with five players drafted in 2006 and another five in 2007.