 Whelan signed a short-term deal with League One club Fleetwood Town on 24 January 2020, joining until the end of the season.In October 2000, Whelan played for the Republic of Ireland under-16 national team in a qualifying tournament in Riga for the 2001 UEFA European Under-16 Championship where he came up against Andrés Iniesta.He represented the Republic of Ireland Under-20 team at the 2003 FIFA World Youth Championship and has been capped 14 times by the Irish Under 21s, captaining the side on many of these occasions.