 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.