Cooper hung up his playing boots in 1996 and moved into management. He began this second career at another Victoria Park, home of Ross County. The Staggies had been voted into the Scottish League just two years earlier after enjoying some success in the Highland League, and were looking to establish themselves among the bigger boys. With Cooper at the helm they did not disappoint. County won the Division Three title in 1998/99 and were promoted again twelve months later after finishing third in the Division Two. Cooper`s reputation was growing. He kept the Staggies in the second tier for a couple of seasons but resigned in November 2002 after a run of poor results began to affect his general health.
Meanwhile in the north east of England, Pools were looking good for promotion under the stewardship of the newly-appointed Mike Newell, who had taken over the reins following the departure of Chris Turner to Sheffield Wednesday. Newell`s side eventually finished the season in second place but the club`s board decided that a new man was needed for a crack at the higher division. That new man turned out to be Neale Cooper. His name hadn`t been mentioned on any grapevine and his appointment was every bit as much of a surprise as Newell`s had been. `Neale Who?` was a common question among Pools fans.
Cooper`s time at Victoria Park was a resounding success. A fierce and passionate touchline presence, he added some inspired signings to the promotion squad and wasn`t afraid to give some of the youth team graduates their chance in the first team. Unfancied Pools made it to the playoff semi-finals in his first season in charge, and were desperately unlucky to lose out to Bristol City. The following season was even better. With Adam Boyd in the form of his life, and the superb Joel Porter (a Cooper find) acting as an ideal partner for him, Cooper`s side looked good for reaching at least the playoffs once more. Though struggling to pick up points on the road, the form at the Vic was outstanding, with ten straight wins between September and January keeping the team in with an outside chance of automatic promotion. From then things began to unravel slightly. The home form fell away and a top six spot no longer looked quite so certain. With one game remaining, Pools needed a point at Bournemouth to clinch the last playoff spot. Defeat would end any hopes of promotion. With just three days to go before this crucial game, Pools fans were hit with sensational news: Neale Cooper had left Hartlepool United.
So what happened? Was this a reoccurrence of any problems that had marked his last days at Ross? Was it a falling out with the board? A falling out with senior players? The rumour mill went into overtime but the statement from the club revealed nothing beyond the familiar `mutual consent`.
A lot happened in the next half-dozen years. Pools of course made the playoffs, losing out in extra time in the final. Cooper`s assistant Martin Scott took over as manager, but lasted less than a season; Pools were relegated and then promoted in record breaking fashion; Chris Turner returned, first as Director of Sport and then as acting manager, to much less successful effect than first time around. When Turner left once more, the respected first team coach Mick Wadsworth reluctantly steered the ship for a while before being dismissed in December 2011. Pools were looking for a new manager again. This time around there was no talk of `Neale Who?” There was much speculation in the newspapers and websites, many names were mentioned including Dave Penney, Phil Brown, Michael O`Neill, Mark McGhee, Jim Magilton and Brian Laws. But the name of Neale Cooper was a tantalising whisper. The former boss had been out of work after spells at Gillingham and Peterhead. He had been a guest of the club earlier in the year so any six-year-old rumours of disagreements were presumably no longer relevant, if they ever were. At the home game against Colchester, as Pools lost at the Vic for the eighth successive match, sections of the crowd chanted `We Want Neale Cooper Back`. A couple of weeks later they got their wish. Cooper was unveiled as the new first team coach on 28th December 2011.