The 31-year-old, who joined the League Two club in 2012, had been suffering with the injury during the opening few weeks of the season.
"The irony is we didn't think he was that bad and he played two games with his knee as it was because we needed him to," manager Paul Tisdale told the Western Morning News.
"I have to make that point - the fact that he carried on and played even though he was in a lot of pain or stiffness. He felt compromised with his knee, but he carried on."
Exeter are currently in 20th place in the League Two table after taking nine points from their opening nine games of the season.