On 1 July 2006, as a free agent, Gerber signed a contract with the Ottawa Senators. However, he struggled throughout the season and was replaced as starting goaltender by Ray Emery. That season, Emery led the Senators to their first appearance in the Stanley Cup Finals, where they would lose to Gerber's former team, the Anaheim Ducks. It was Gerber's third appearance in the Stanley Cup Finals in five years. Gerber began the 2007–08 season as the Senators' starter when Emery was sidelined after off-season wrist surgery. His play was inconsistent and Emery resumed the starting job once he was healthy again. However, after the team suffered a rapid decline in the standings and head coach John Paddock was fired and replaced by general manager Bryan Murray, Murray declared Gerber as the starting goaltender for the remainder of the season. Gerber entered the 2008–09 season in that role, but his uneven play continued and he was eventually supplanted by the newly signed Alex Auld. On 22 January 2009, Gerber was placed on waivers after having been sent down to the Senators' then-American Hockey League (AHL) affiliate, the Binghamton Senators.