The 23-year-old, who is on the transfer list after asking to leave Sincil Bank, will have surgery on Monday after colliding with a team-mate in training.
Imps boss Keith Alexander said: "It's terrible news because he has had such a good season for us. It was such an innocuous incident.
"He simply went up for a high ball through a crowd of players. It's too early to say when he might be back."