Coach Craig Bohl said Monday it's too early to say whether Allen will miss this weekend's game against Fresno State.
"It may come down to a game-time decision," he said.
Bohl described the injury as involving "soft tissue" and said Allen is receiving treatment. He described Allen's status as day-to-day.
"Structurally, the information that we were given, is that he's in good condition there and it will just be a matter of time to when he's able to come back and return, and we're in hopes it's sooner than later," Bohl said.
Bohl said he believes Allen will be cleared to practice sometime this week.
Allen was not available for comment Monday because he was receiving treatment on the shoulder.
Allen injured his throwing shoulder Saturday during Wyoming's 28-14 win at Air Force.
Allen left the game following Wyoming's first offensive series of the second half after attempting one pass that was incomplete. Backup Nick Smith finished the game.
"He threw the one ball, and he didn't have full strength," Bohl said.
Allen has thrown for 1,658 yards this season with 13 touchdowns and six interceptions. He has rushed 84 times for 207 yards and five touchdowns.
Allen's arm strength and ability to throw on the run have drawn a lot of attention from pro scouts. He has been considered one of the top quarterback prospects for next year's NFL draft.