During the 2006 pre-season, Lynch underwent mental therapy aimed at improving his marking. His form improved considerably, and he took 43 marks in the first eight rounds of the regular season. During the season he kicked four goals in one game, five in another, and a career-best eight in the round 20 match against the Brisbane Lions. He kicked a total of 65 goals for the year, making him the first Eagle to kick over 50 goals in one season since Scott Cummings. In the 2006 finals series, he kicked more goals than any other player for that year. He was the Eagles' leading scorer in the 2006 grand final, kicking three goals in the Eagles' one-point victory.