The one-time Republic of Ireland international, 50, a crowd favourite during his playing stint with the club in the Nineties, had served as a first-team coach under manager Tony Pulis, who left the club last Friday.
Fellow senior coach Jonathan Woodgate, said to be interested in stepping up to a head coach role and the favourite in the betting to replace Pulis, remains at the club.
Meanwhile, vastly-experienced ex-Leeds United and Sheffield United assistant Sam Ellis, 72, who linked up with Pulis as his deputy last summer, has also left Boro.
Boro will not be renewing the contract of goalkeeping coach Jonathan Gould, while performance coach Tim Exeter and analyst Carl Blakemore have departed.
Promotion-winning captain Nigel Pearson has revealed his interest in the vacant position, having gone close to landing the job prior to the appointment of Garry Monk in June 2017.
Ex-Leicester City and Hull City chief Pearson, who captained Boro to the top flight under Bryan Robson in 1994-95 and 1997-98 and also led them in three cup finals, is back in England after a spell in Belgian football with OH Leuven and is keen to return to management.
Sheffield-based Pearson, 55, said: “Middlesbrough is a football club that anyone in my position would have to contemplate.
“It is a fantastic club and Steve Gibson is a fantastic chairman.
“Whoever gets the job will be taking over a superb club with all the structures in place to be successful.
“I was a bit surprised that it did not work for Tony Pulis, but it shows you how difficult it is to be successful in the Championship.
“Things do not always run smoothly, so it is about hopefully getting the fanbase to buy into the challenge. Sometimes you have to learn to enjoy the journey.
“In the modern game, it is easy to lose contact with the supporters. I have very fond memories of my time at Middlesbrough and I know it is a passionate area where the club is so important to the community and to the fans.”
Former Boro defender and current Ajax second-team coach Michael Reiziger is reportedly among the contenders, as is former manager Aitor Karanka.