Griffin coached the colts teams for Redcliffe (1995–97), winning the premiership in 1997. The following year he moved to Brisbane Norths, taking them to the colts premiership in his first year there, and also coaching the Queensland under 17s representative team in 1998. After another colts premiership with Norths in 2000, Griffin joined the coaching staff of the NRL's Melbourne Storm and was Chris Anderson's then Mark Murray's assistant in 2001 and 2002. Returning to Queensland, he coached the Souths Logan Magpies in the Queensland Cup from 2003 to 2004. He then joined the Redcliffe Dolphins, coaching them from 2005 to 2007 and winning the competition with them in 2006. He also coached the Queensland Residents side in 2007.
Griffin coached the Brisbane Broncos' under-20s side to the 2008 Toyota Cup season's grand final. He was appointed as assistant to head coach Ivan Henjak for the 2010 NRL season, in which the Broncos failed to make the finals series for the first time since 1991.
Less than three weeks from the beginning of the 2011 NRL season, Griffin became the third ever coach of the Broncos when he was unexpectedly announced to be replacing Henjak. After losing their first match, the Broncos went on to win seven matches in a row, to be sitting equal top of the ladder with the St. George Illawarra Dragons at the conclusion of Round 8. Griffin employed a policy of resting key players such as Darren Lockyer and Sam Thaiday after mid-season representative matches and Brisbane's ladder position slipped. However they returned to the top four after the 2011 State of Origin series. The Broncos finished the regular season in third place, their best finish to the regular season since their last premiership in 2006. Griffin then took them to within one match of the grand final. However without injured captain Darren Lockyer Brisbane were knocked out of contention by eventual premiers, the Manly-Warringah Sea Eagles.
During the 2014 NRL season it was announced that Griffin would not be head coach of the Broncos the following season due to the return of the club's foundation coach, Wayne Bennett.