The Broncos did not start the 2006 season well, suffering a 36–4 defeat by the previous year's runners-up, the North Queensland Cowboys in the first round.
Round 8 saw Brisbane produce their biggest comeback in the club's history when they came from 18–0 down at halftime to win 30–28 over the Canberra Raiders.
But the year's biggest upset came when the team, missing key players through State of Origin, lost to the last-placed and previously winless South Sydney Rabbitohs 34-14 in Round 14.
However, strong performances against the competition leaders Melbourne Storm (losing 18–12) and a resounding victory against the Canterbury Bulldogs 30-0 the following week saw a return to form.
Brisbane was heading into the finals with momentum not seen since 2000, but lost to the St. George Illawarra Dragons 20-4 in what was the highest attended Broncos game ever played at Suncorp Stadium at the time.
Captain Darren Lockyer also became the Broncos' highest point-scorer with 1,077 (breaking Michael De Vere's record of 1,062 points).