Agnew had a coaching post with Boro's academy teams six years ago and has since been on the coaching staff at both Leeds and Hartlepool.
He told BBC Radio Cleveland: "It's great to be back at Boro, where I first started my coaching career.
"I'm really looking forward to working with Gareth Southgate and all the lads. Everyone has made me feel at home and I can't wait to get started."
