 Whelan started his career with Manchester City joining from Irish feeder club Cherry Orchard in 2001.He made a solitary appearance in the UEFA Cup coming on as a substitute for Paul Bosvelt against Total Network Solutions in August 2003, before joining Bury on a one-month loan the following month.After appearing in the Republic of Ireland's 2003 FIFA World Youth Championship campaign in November and December, he returned to Bury on another one-month loan on 24 December 2003.