The 22-year-old, who has played over 150 times for his boyhood club, underwent surgery on a broken ankle sustained during the 2-2 draw with Barnet on December 29.
And manager Paul Tisdale expects that the injury will end the midfield regular's campaign, much to the frustration of his team-mates including Irish forward O'Flynn.
"It is a massive disappointment," he told Press Association Sport.
"His ankles had been taking a bit of a battering and we just thought it was something similar. But to get a break at this time of the season, when he had just scored and was starting to fly, is so disappointing.
"It leaves a big hole but we have some good players here who are ready to step in and take his place."
Sercombe had already made 23 appearances this season for the npower League Two promotion hopefuls and he had been finding his form before suffering the injury last month.
And O'Flynn explained how down the City youth product has been since going under the knife.
"He is down in the dumps," O'Flynn said. "I was talking to him during the week. I said to him we seemed to lose it after he went off against Barnet, to try and cheer him up!
"But like I said to him he will be back better and stronger."
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