Carayol hyper-extended his knee during Middlesbrough's 3-1 victory over Preston North End in the Capitol One Cup but Mowbray has backed the 23-year-old to return stronger after a four-month absence.
Mowbray told BBC Tees: "He'll be a huge loss for us. I'm hugely disappointed for him.
"He has started his career so well and hopefully he'll come back stronger."
Carayol signed for Middlesbrough from Bristol Rovers during the summer.