Wilson played his 150th WAFL league match in Round 12, celebrating the milestone with a seven-goal haul in a victory over East Fremantle. The following week, Wilson kicked eleven goals in East Perth’s upset win over Claremont, becoming the first Royal to kick a bag of ten or more goals in a game since 1996. With three rounds remaining, Wilson revealed that 2006 would be his last season for East Perth owing to a major back problem that allowed him to train only one night per week. He finished the season with 74 goals, including six in the final round to be awarded the Bernie Naylor Medal as the leading goalkicker in the WAFL. He also won his second F.D. Book Medal.