Keeton missed most of last season after tearing two knee ligaments in a game against BYU.
This season, Keeton was injured in a victory over Wake Forest on Sept. 13 and missed the Aggies' loss to Arkansas State a week later. Darell Garretson, a sophomore, started against Arkansas State and threw for 268 yards and two touchdowns.
Utah State plays at No. 18 BYU on Friday night.
Keeton, a senior, could apply for a medical redshirt and return to Utah State for another season. The 6-foot-2, 200-pounder from Houston could also enter the NFL draft.
For his career, Keeton is second in Utah State history in touchdown passes (58) and completions (568) and third in yards passing (6,387).