In July 2006, after his release by Grays, Hooper went on two trials. Firstly to League Two club Barnet, then to Championship club Southend United, where he was given a one-year contract by manager Steve Tilson the following month. On 24 October, Hooper scored twice in a 3–1 League Cup win over Leeds United. He went on to make 18 appearances for Southend in the Championship, although only two were starts. On 15 March, Hooper joined League One club Leyton Orient on loan for the rest of the season. Tilson said that this loan would allow him to assess whether Hooper merited a new contract and would give the young striker experience. Hooper was recalled from loan on 1 May before, already relegated, Southend's last match of the season. A number of players were out injured for the match and, five days after his recall, Hooper started in the 4–1 defeat to Southampton.