Naitanui made his AFL debut for West Coast in round 12 of the 2009 season, against . He played ten games in his debut season, and received one Brownlow Medal vote for a three-goal game against . In his second season, Naitanui played every game, primarily as a back-up ruckman to Dean Cox, taking over the position of Mark Seaby, who was traded the previous season. Having started the season as the favourite for the AFL Rising Star, Naitanui finished 5th overall. In the 2011 season, he played 23 games, including his first finals matches, and was also nominated for Mark of the Year. He was named in the All-Australian team the following season, as the first-choice ruckman.
