Prentice left Perth Glory at the end of the 2007/08 season, after failing to negotiate a new contract. He was signed by Sydney FC for the 2008/09 season, on a 2-year deal with Sydney FC. He scored his first goal for Sydney in their first 2008 preseason cup game against Queensland Roar at Campbelltown Stadium in their 2-1 Victory. He scored off the free kick that resulted in Queensland's Seo Hyuk-Su being sent off for a sliding tackle against Sydney's Alex Brosque. Prentice played his first A-League match as a Sydney FC player on 30 August 2008 at the Sydney Football Stadium against his old club Perth Glory. Prentice played the full match in which Sydney FC won 5-2. Prentice decided to end his contract 3 months early with the Sky blues in early 2010.
