The 18-year-old Wales Under-21 right-back stands as one of the few bright sparks during a trying season at Ewood Park after breaking into the first team during Henning Berg's brief and unsuccessful stint as manager.
Henley was initially stuck by hamstring trouble during January's FA Cup third-round win over Bristol City.
Following almost two months on the sidelines, he returned to the side in recent weeks only to break down at Millwall in Sunday's goalless FA Cup quarter-final.
Speaking ahead of Wednesday night's replay, Rovers manger Michael Appleton said: "Poor Adam, he's done his hamstring again. A grade two (tear) and it looks quite a bad one.
"It's probably the end of his season, which is disappointing because he's a young player that obviously we rate very highly.
"I haven't seen much of him because of injury - it's probably the same with a few of the players since I've been at the club."