Mark Smith criticised the referee's decision. Under new manager Paul Sturrock the team managed to finish in 5th position in 2004–05 claiming a play-off place where they defeated Brentford to reach the final. Whelan was voted "man of the match" in the League One play-off final against Hartlepool United at the Millennium Stadium in Cardiff after scoring the match-winning third goal for Wednesday. After Wednesday won promotion to the Championship, Whelan was trialled as captain by Paul Sturrock after regular captain Lee Bullen was injured. Wednesday were able to avoid an instant return to the third tier in 2005–06 as they finished in 19th position, Whelan playing in 46 matches that season scoring once, which came in a 2–1 defeat against Watford. In July 2006, Whelan was placed on the transfer list by Sturrock following increased competition for places in the Wednesday midfield after the arrival of Wade Small, Kenny Lunt and Yoann Folly. He was subsequently removed from the transfer list by the following manager, Brian Laws. Whelan repaid the faith shown in him with seven goals. He then went on to win a number of player of the year awards for the club's 2006–07 season. His performances led to manager Laws entering into contract negotiations with Whelan. Sheffield Wednesday rejected bids for Whelan from both Burnley and Plymouth Argyle in January 2008. However, a £500,000 bid from Stoke City was accepted on transfer deadline day. Stoke City Whelan joined Stoke City on 30 January 2008 for £500,000 signing a three and a half-year contract. He made his first Stoke City appearance in a Championship match against Cardiff City on 2 February 2008 when he came on as a substitute in the 82nd minute for Mamady Sidibé. Whelan made his first Stoke City league start the following match in a 4–2 victory against Wolverhampton Wanderers. He scored his first goal for Stoke in a 2–1 home defeat to Crystal Palace on 7 April 2008. Whelan played 14 times for Stoke City in the 2007–08 season as Stoke finished 2nd and were promoted to the Premier League. Whelan started the club's first match in the Premier League against Bolton Wanderers. Whelan did not have a good match and as a result he did not feature much in the first team, only playing in League Cup fixtures and even reserve matches. Despite this setback, Whelan was still a regular in the