Born in Reddish in Stockport,[2] Whelan began his career at Ipswich Town, signing professional terms with the club on 2 July 1990.
[3] He made his Ipswich debut in a Full Members Cup first round match against Bristol Rovers on 2 October 1991.
[4] He spent most of the 1991–92 season playing for the reserves in the Football Combination, not making his league debut until 4 April, when he scored the first goal in a 2–1 win at Southend United.
He also became an England U21 international, and was a member of the Great Britain team that competed in the World Student games in July 1993, qualifying as he was completing an accountancy degree at the University of East Anglia.
In March 1995 he was sold to Middlesbrough for £300,000,[3] with his final Ipswich game being a 3–0 defeat to Norwich City in the East Anglian Derby.