Debuting in 1997 as a 17-year-old, the young Whitnall was recruited in the 1996 AFL Draft under the father–son rule, with his father Graeme having played 66 games for Carlton in the 1970s and 1980s.

He became a vital part of Carlton's forward line, and in Round 17, 1998 against the Western Bulldogs, the then-19-year-old Whitnall became one of the youngest players to kick 8 goals in a game.

He capped off a solid 2006 with victory in the Blues' best and fairest (the John Nicholls Medal), and at the age of 27, Whitnall became the second youngest Carlton player (after Robert Walls) to play 200 AFL games.

At the completion of the 2007 season, concerns by the club about his degenerative knee being able to stand up to the pressures of AFL football forced Whitnall into retirement, bringing his 11-season, 216 game career at Carlton to an end at 28 years of age.

Whitnall was recruited by NTFL side the Palmerston Magpies after being delisted by Carlton and played in two of the club's matches in the 2007/08 season, kicking several goals.