Despite rumoured interest from Carlton, Shirley was immediately redrafted by the Crows with pick 53 in the 2002 AFL Draft and placed on the club's rookie list.
This included a noteworthy shutdown of future Brownlow Medallist Chris Judd in the Crows' Elimination Final victory over the West Coast Eagles.
The 2005 AFL season proved a watershed year for Shirley as he became the club's primary tagger following the decision by Tyson Stenglein to return home to Perth at the end of 2004.
[6] In 2006 Shirley began to develop his ballwinning skills, averaging 16 disposals per game and leading the club in Hard Ball Gets with 75 for the year.
At the conclusion of Round 5 Shirley won the AFL Army Award for the most courageous act of that week's matches, for his last-ditch spoil going back with the flight of the ball deep into the last quarter of the Crows' 1-point loss to Fremantle.
Dropped for the first few games of the season, Shirley did return in round 11 but could not hold his place on a consistent basis and was in and out of the side, as quicker and more attacking players such as Michael Doughty and Nathan van Berlo were favoured in negating roles.