Gilbert, a heralded recruit and former McDonald's All American, played the first six games of the season. He injured his left shoulder in a loss to Michigan State at the PK80 Invitational on Nov. 24; he was on the court for 17 minutes against Arkansas two days later, and has not played since.
UConn says its medical staff and orthopedic surgeon Dr. James Andrews have recommended another surgery.
Coach Kevin Ollie says the doctors anticipate that Gilbert will make a complete recovery in time for the start of the 2018-19 season.
Gilbert also missed the majority of his freshman campaign due to a torn labrum in his shoulder, playing just the first three games. He was granted an extra year of eligibility following last year's injury.
He also had two significant shoulder injuries prior to arriving at UConn.
"As we have said all along, we are going to listen to Alterique and do what is best for him and his family," UConn coach Kevin Ollie said. "If that includes surgery, then we will give him all the support he needs and welcome him back on the court next season. Meanwhile, he will have the chance to see the game from a different perspective. I know he will continue to be a great team leader -- during practice, during games and off the court as well."
Gilbert, who was selected as the American Athletic Conference's preseason newcomer of the year twice, had averaged nine points, four rebounds and 2.8 assists this season.
UConn has struggled again this season and will go into Saturday's matchup against Wichita State with a 7-5 record.
The Associated Press contributed to this report.