At the start of the 2009–10 season, Queens Park Rangers had a £1 million rejected for Hooper. Coventry City were also rumoured to be interested in the striker. On 15 August, Hooper scored twice in a 3–2 win over Derby County. Scunthorpe manager Nigel Adkins said that he thought Hooper was a "massive threat" to the opposition and that he was worried that other teams would try to sign him before the end of the transfer window. On 22 February, captain Cliff Byrne, described Hooper as the kind of striker who could "create something out of nothing". He also stated that he hoped Hooper would stay at the club but if he did leave it would be for a lot of money. This was just after Hooper had scored in a 2–2 draw with Watford, taking his seasonal tally to 13. He scored a hat-trick against Bristol City on his return from a groin injury on 17 April 2010, and added a further two goals at Doncaster Rovers a week later. He scored 20 goals in 39 appearances in all competitions in the 2009–10 season, including 19 in 35 in the league, where he finished as third-top goal scorer behind Peter Whittingham and Nicky Maynard who both scored 20.