Hooper started his career at non-League Grays Athletic in 2003. While there he won the 2004–05 Conference South, as well as the FA Trophy twice in 2005 and 2006. After this Championship club Southend United signed him on a free transfer in 2006. He was loaned out twice by the club, on a three-month loan to League One club Leyton Orient in 2007 and a six-month loan to League Two club Hereford United in 2008. Scunthorpe United signed him in 2008, for a fee of £175,000. After two years he was signed by Celtic for £2.4 million. In his first season with the club he was the top scorer and also won the 2011 Scottish Cup.
Hooper has scored in the Premier League, Championship, League One, League Two, FA Cup, League Cup, Football League Trophy, FA Trophy, UEFA Champions League, UEFA Europa League, Scottish Cup, Scottish League Cup and the Scottish Premier League, the first and only player to achieve this feat. On top of this, he has also scored in the Conference National and the Conference South.