On 15 March 2007, Hooper moved on loan to League One club Leyton Orient. Two days after joining the club he scored in a 2–2 draw with Oldham Athletic after coming on as a substitute. A week later, he scored against League One leaders Scunthorpe United in another 2–2 draw. Hooper made two more appearances for Orient, before being recalled to Southend on 1 May, when the club activated a 24-hour return clause in his contract. Orient manager Martin Ling said that he thought Hooper had done well during his loan spell with the club and that he would monitor the progress of the young striker.