Hughes and his assistant Micky Barron left the club on May 9 and they are to be replaced by a former Middlesbrough double act of Cooper and Craig Hignett.
Cooper, 46, becomes the club's sixth manager in four-and-a-half years and his main aim is to get the club back into League One after they were relegated under Hughes last season.
The former Boro and Nottingham Forest defender has forged a coaching career since retiring from the playing ranks in 2006.
He briefly became caretaker manager at the Riverside in 2009 when Gareth Southgate left the club and returned to the club's academy in 2011 after a spell as assistant to Peter Jackson at Bradford City.
Striker Hignett ended his playing career with a brief spell at Victoria Park in 2007 and was also part of the Academy staff at Middlesbrough.