In September 2009, Webber signed for Portsmouth who were looking for attacking options. He signed outside the transfer window as he was a free agent. He scored his first goal for the club in a 3–1 League Cup victory over Carlisle United on 22 September. Webber scored his first Premier League goal for Portsmouth in a 1–1 home draw against West Ham United on 26 January 2010. He was ruled out for the remainder of the season after rupturing cruciate ligaments in a game against Tottenham Hotspur two months later. He received a runners-up medal for the 2010 FA Cup Final defeat to Chelsea, though he was unable to take part in the final itself. Webber remained in the treatment room for much of the 2010–11 campaign, before he made his return to action in a 2–0 defeat to Reading at the Madejski Stadium on 2 April, making a cameo appearance for the last five minutes. His contract was not renewed at the end of the season.