The defender, on loan at Bristol Rovers from Leicester, was stretchered off during Saturday's 2-2 draw against Aldershot and despite initial hopes it would be nothing serious, scans have found the knee injury to be worse than first anticipated.
Bolger rejoined the League Two club on loan for a third time on transfer deadline day, with the 20-year-old Irishman due to remain at the Memorial Stadium until January 1.
Rovers boss Mark McGhee told the club's official website: "I'm absolutely gutted for Cian, and the fact is I think he injured himself being as committed as we had asked him to be. He showed where his commitment lies, and it's a great shame for him to be out at this moment in time.
"The prognosis is that he will be out for three months and we hope he will make a full recovery and be back playing by Christmas, fingers crossed. He will go back to Leicester for his rehab and, hopefully, be back here before his loan period expires.
"He was going to be a really important player for us. We tried hard all summer to get him here and eventually managed to do that and, as everyone has seen, he has been absolutely brilliant in the short time he's been back with us. He showed how important he was going to be for us and we are gutted for ourselves but, more than anything, for Cian."