At the start of the 2008–09 season. Hooper, along with three other strikers, was listed for transfer as Tilson looked to re-build his attack. Hereford had a bid accepted for Hooper after his successful loan spell, but could not afford to match the larger transfer fees offered by other teams. Several other League One clubs were interested in him. Cheltenham Town had a bid accepted but Hooper eventually decided to move to Scunthorpe United. He scored just four goals in 44 appearances during his time at Southend. Although he did have two successful loan spells.