Allen, who finished fifth in the final of the 110m hurdles at last month's Rio Games, is reported to have suffered a torn anterior cruciate ligament.
Allen, a wide receiver for the University of Oregon, is unlikely to play again this season, several US media reports said.
The injury is a cruel blow for the talented 21-year-old who in Rio talked about the possibility of pursuing a National Football League career while continuing to compete in elite track and field.
Allen injured his right ACL returning a kickoff in 2015, and missed the following track and field season.
However, he recovered from that injury to win a spot on the US Olympic team with a first place finish at the national trials in Eugene in July.
