The 2006–07 season is Sydney FC's second season of soccer in Australia. Sydney FC contested in the 2006–07 A-League, and after winning the inaugural A-League Championship in 2005–06, competed in the 2007 AFC Champions League as one of Australia's two representatives.

After winning the A-League Championship in his first season with the club, head coach Pierre Littbarski signalled his intentions to remain with Sydney FC for the following season in April, whilst the club indicated that an "in-principle agreement" with Littbarski had been finalised. In May 2006 however, it was revealed that Littbarski would not accept an estimated A$250,000 pay cut to his original contract and thus decided to leave Sydney FC. Two months later, Sydney announced that they had agreed to terms with Motherwell F.C. manager and former England international Terry Butcher, who would sign a two-year deal.

During the off-season, Sydney released Andrew Packer from the final year of his contract for him to return to his home state to play for Queensland Roar, whilst signing Alex Brosque (Queensland – 3 years) and Jeremy Brockie (New Zealand – 2 years). 19-year-old Ruben Zadkovich, who was signed as short-term cover for Ufuk Talay late in the 2005–06 season, also upgraded to a two-year full-time contract with Sydney.Matthew Bingley was released from the squad due to salary cap restrictions.

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