The 46 year old spent ten years on Teesside and was Middlesbrough's club captain before ending his playing days and embarking on a managerial career which has seen him at Hibs, West Brom and Celtic.
Mowbray replaces former Coventry City player and manager Gordon Strachan who left Middlesbrough last week by mutual consent.
Mark Venus will be Mowbray's assistant, it has been announced.