Timonen is being treated for the blood clots in his home country of Finland and a return date has not been set.
The 39-year-old veteran signed a one-year contract extension in June to stay with the Flyers for an eighth season.
Timonen has 232 assists and 270 points with the Flyers -- ranking him third all-time among Philadelphia defensemen in both stats. He has 117 goals and 454 assists for 571 points in 1,092 career games with the Flyers and Nashville Predators.
In 77 games last season, Timonen posted six goals with 29 assists for 35 points.