Hignett was working as a part-time academy coach at Rockliffe Park before moving to Pools last May, but will be back at his old club this morning, with Boro hoping his charisma and local knowledge will provide a much-needed lift amongst a sequence of bad results and a run of over 11 hours without a goal.
However, it is understood Pools officials are unhappy at the manner of his departure and the nature of a curt club statement released last night indicated as much.
It read: "The Club wishes to advise that late this afternoon Assistant Manager Craig Hignett has handed in his notice.
"Middlesbrough Football Club have advised the Club's Chief Executive Russ Green that Craig will not be working his notice period for Hartlepool United and will be starting work at Middlesbrough on Tuesday 4th March.
"The Club has no further comment.''
Cooper has long hoped to have a blossoming relationship with his former club. Pools currently have Christian Burgess on a season-long loan and his development and improvement has been marked.
They have also had Matty Dolan and Luke Williams on loan, but both have been recalled when Pools hoped to keep them for longer. Dolan has since gone to Bradford, while Williams was surprisingly left out of Karanka's match-day squad for the weekend defeat at Sheffield Wednesday.
Boro have been without an assistant since Karanka's appointment in November last year.
Mark Venus, who was Tony Mowbray's assistant left the club a while after Mowbray's sacking and Karanka has been using Jamie Clapham, who will now revert to his role as Senior Professional Development Phase coach, looking after Boro's under-21 side, as his assistant.
Karanka previously said: "I said at the beginning I wanted an assistant, like I was to Jose (Mourinho). I knew all about Real Madrid and helped him in that way. I asked the club for an assistant who knows the league, the club and the players."
Now, with Hignett's appointment, Boro and chief executive Neil Bausor have made their move, with Hignett fitting those characteristics.
Hignett was deep in conversation with Pools chairman Ken Hodcroft at Victoria Park on Saturday after the 3-0 win over Torquay United.
Cooper and Hignett have proved a good partnership, since the manager opted for the former Premier League striker when he was appointed.
He recently admitted: "The relationship between and Craig is brilliant because I'm smiling and I love seeing players defending and blocking and clearances off the line and stuff like that Craig says 'I hate all that, I want to see us being creative at the other end of the pitch' - and that is contrast is brilliant.''
Cooper will now start to look for a new assistant. Sam Collins could get a chance to make the role his own, after the centre-half took up additional coaching duties this season, which included taking charge of the reserve side on occasions.
Pools second string at at Hull this evening, with Collins set to be in control.
Well-respected in the dressing room, and also by Cooper, Collins is in the process of taking his coaching badges.
Collins performing so well at centre-half since his recall to the side in recent weeks, earning regular praise from Cooper for his professionalism throughout the season, which has been spent on the sidelines fo rthe majority.
Luke James has 14 goals to his name this season, Saturday's goal was his third headed strike.
The talented teenager has developed into an all-round striker this season, scoring a range of goals - tap-ins, headers, volleys and shots from distance - and he puts his improvment down to Hignett's tutelage and training sessions.
Speaking after his stooping header in Saturday's win, the forward admitted: "I'd have taken one headed goal at the start of the season! It's like when you hit a nice strike, you sort of know if it's going in.
"A lot of it is down to the shooting practice I do with Higgy.
"He likes to do loads of different drills and I put it (the improvement) down to practice really.
"If I have a career as good as his, I'll be happy.
"He is always giving me advice, stuff like waiting for the keeper to go down and lift the ball over him.
"He gives me lots of pointers and stuff to work on, it's a big help.''
Now Boro's shot-shy forwards will hope for a similar boost from the man who scored 48 goals in 194 appearances for the club from 1992-1998.