The 2008–09 season started with a last 32 loss to Barry Hawkins in the Northern Ireland Trophy and losing in the quarter-finals of the Shanghai Masters to Mark Selby. At the Grand Prix, he lost in the second round to Ronnie O'Sullivan, a repeat of last season's final. At the 2008 UK Championship, he beat Barry Hawkins in the first round, followed by Matthew Stevens and Joe Perry. In the semi-finals, Fu defeated Ali Carter after trailing 2–5, he levelled to 6–6 and won 8–6. In the final, Shaun Murphy defeated Fu 9-10. He suffered a first round defeat to John Higgins at the Masters. At the 2009 World Snooker Championship, he advanced to the second round by beating Joe Swail 10–4 before losing 3–13 to Murphy.