The 22-year-old damaged ankle ligaments during the club's 4-1 defeat at Arsenal on Tuesday, which saw the Latics relegated from the Premier League.
McManaman was the star of Wigan's 1-0 FA Cup final win over Manchester City and was rewarded for his recent excellent form with a first call-up to Stuart Pearce's England squad for the tournament in Israel next month.
But he will now miss Wigan's final game of the season at home to Aston Villa and is in a race to be fit for the start of next season.
"It's good news because we expected the worst," said Wigan boss Roberto Martinez.
"He doesn't need surgery which is really positive but it does mean he will be out for the best part of three months.
"That will put him out of the Under-21s which is a real shame as he really deserved to finish the season with that experience.
"Callum is disappointed but it's such a joy to see him playing his football. It's a joy for everyone. For me he's been one of the sparks of the season, and not just at Wigan.
"He's a real diamond of English football. He's got no reason to feel down at all."
McManaman was named Wigan's young player of the year on Wednesday following a season that saw him score six goals in 30 appearances.
The former Everton youth player has been linked with a move to Liverpool in the wake of Wigan's relegation.
But Martinez added: "If one player needs to stay at the club and become an important part of this football club, it's Callum.
"He's been a phenomenal player for us but he's someone who, at 22, needs to work on certain aspects to become the player he can be.
"He will be a top, top player, and probably the next 10 months are vital for him to be perfect in the programme that he has to fulfil.
"Probably, the Championship, for him to play week in, week out and have an important role, it will be the perfect challenge for him."