Crowley was first drafted by Fremantle in 2002 with selection 55 at the national draft. At the end of 2004, having only played WAFL football for Subiaco, he was delisted. However the club gave Crowley a second chance and re-selected him with their 3rd pick in the rookie draft. Good form with Subiaco in 2005 led to his elevation to the senior list when both Robert Haddrill and his replacement Michael Warren were placed on the long term injury list.
His debut was notable in that he became only the 3rd Fremantle player to kick 3 goals on debut (along with Leigh Wardell-Johnson and Paul Medhurst), and those goals helped Fremantle to record their first ever win at Skilled Stadium in Geelong. His continued good form in the second half of the 2005 season including 4 goals against Carlton at the MCG saw Ryan elevated to the senior list for the 2006 season. Early in the 2006 season, Ryan got a heavy blow to the face during a shepherd from Byron Pickett, and received a broken cheekbone. Crowley continued to improve throughout the 2007 season, having gathered 319 disposals in 19 games and earning a regular spot in the Fremantle midfield as a winger/onballer who can kick goals.
In 2009 Crowley injured his foot in the Round 6 Western Derby and was ruled out for between three months and the entire season. He didn't return to the Fremantle side until the first round of 2010. He played the first 16 games of the season, before injuring his knee against Melbourne, missing the next six games. He returned for Fremantle's two finals, after proving his fitness in a dominant display in the WAFL for Subiaco, kicking seven goals.
He continued to nullify the opponent's best midfielder each week and won the Doig Medal in 2012 as Fremantle's best and fairest player. In 2013 he was suggested as being worthy of selection in the All-Australian team, but was overlooked.
Crowley did not play in Fremantle's 2015 pre-season games or in Round 1 of the 2015 season. The club explained that this was due to "working through an issue". Three days later it was revealed that Crowley had tested positive to a banned substance after Fremantle's 2014 Round 17 win over Greater Western Sydney and had been serving a provisional suspension since mid September 2014. The banned substance has not been named, but is thought to be from a painkiller that was not prescribed by the club doctor. He was set to appear before the AFL Tribunal on May 1st 2015 but the hearing was pushed to May 18th.