Whalley began his football career at Crewe Alexandra, making his club debut in a 4–1 League Cup first round win over Rochdale at Gresty Road on 18 August 1992.
[1] He scored his first two Crewe goals in a 6–1 FA Cup second round victory over Accrington Stanley, played at Blackburn's Ewood Park, on 5 December 1992,[1] and was part of the Crewe side beaten by York City after a penalty shoot-out in the 1993 Football League Third Division play-off final at Wembley Stadium on 29 May 1993,[1] his penalty kick being saved by Dean Kiely.
In July 2002, Whalley joined League Two side Cardiff City, making his debut at Oldham Athletic on 10 August 2002, and playing a further 22 times in a season interrupted by injury.
Whalley was then involved in a contractual dispute over a £50,000 appearance bonus,[9] and had his contract cancelled by the club, signing for EFL Championship side Wigan Athletic in September 2004.
At international level, Whalley was included in a number of Republic of Ireland senior squads under Mick McCarthy[12] but never won a full cap.