On 14 July 2008, Scunthorpe United signed Hooper for a fee of £125,000, rising to £175,000. Hooper signed a three-year contract with the League One club. In the first match of Scunthorpe's league campaign, Hooper scored in a 2–1 defeat at Glanford Park against Leeds United. He scored his first ever hat-trick against, Brighton, on 6 September and netted seven goals in his first seven matches to help Scunthorpe's promotion push. After this teammate Izzy Iriekpen paid tribute to Hooper saying that "As soon as he started training you could see there was something special there." On 28 October, league leaders, Scunthorpe suffered their first defeat in 12 matches as they lost 3–0 to Oldham Athletic. Hooper came off with an injury in this match and it was feared he had broken his foot and may have been out for up to six months. However, scans later revealed that his foot was just badly bruised. He was labelled in the media as the latest from Scunthorpe's "production line for talented young forwards." He scored both goals in a win over promotion rivals Millwall on 31 January 2009. Scunthorpe reached the final of the Football League Trophy and faced League Two Luton Town. Hooper scored the opener but Luton pulled it back to win the match 3–2 in extra-time. At the end of the season Hooper won Scunthorpe's Player of the Year award. He said he was delighted with the team's performance during the season, in which he scored 24 league goals to help Scunthorpe gain promotion. He then set himself a target of 15 Championship goals for the next season. He scored 30 goals in all competitions throughout the 2008–09 season, just three goals short of Billy Sharp's record 33 goals in a season for Scunthorpe.