Timonen and the Flyers faced the Washington Capitals in the first round of the playoffs. Philadelphia was able to win the series 4–3. In the second round of the playoffs, the Flyers played against the Montreal Canadiens and won the series 4–1. On April 30, 2008, Timonen was hit by a wrist shot at his foot by Canadiens defenseman Andrei Markov. He said that he had felt numbness in his foot but he didn't think it was anything but a twisted nerve. On May 8, 2008, a doctor at the Hospital of the University of Pennsylvania who looked at Timonen's foot said that he had found a small blood clot. This stopped Timonen from playing indefinitely and he missed the first four games of the Eastern Conference Finals against the rival Pittsburgh Penguins. He returned in game 5 but the Flyers lost and they were eliminated from the playoffs. On March 5, 2011, Timonen scored his 100th career goal against Ryan Miller of the Buffalo Sabres in a 5–3 loss. On August 5, 2014, Timonen was diagnosed with blood clots in his right leg and both of his lungs. He was ruled out from playing indefinitely and missed the first 62 games of the season.