Morale was low at the North East club after a disappointing Premier League campaign ended in relegation in 2009, but Harper has suggested that Hughton had a dramatic impact in reversing the club's fortunes for the promotion push the following season.
"It was obviously a difficult time at the club, but Chris [Hughton] just gave everybody a clean slate and basically set out what we needed to do," he told reporters.
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"He and Colin [Calderwood] gave us a strategy, broke down that Championship season into little segments, set us targets and we achieved virtually every one of them.
"It can be a long season in the Championship, but Colin had experience of it and the pair of them and Paul Barron worked well together, really gelled the team and forged a fantastic team spirit which got us through a very tough season."
Having won just seven Premier League games in their relegation season of 2008-09, accumulating 34 points and scoring only 40 goals with firstly Kevin Keegan, then Joe Kinnear and finally Alan Shearer in charge, Newcastle under Hughton raced to the second-flight title and automatic promotion in 2009-10 with 30 wins, 90 goals scored and an impressive 102 points to their name.
Yet Hughton was surprisingly sacked in December 2010, leading fans and pundits to question the Newcastle hierarchy after the 53-year-old's fine work at the helm. However, despite the fans' initial doubts over the appointment of Alan Pardew, Harper insists that the 51-year-old current manager suits the ethos of the club and its fans.
"The manager [Pardew] has given credit to Chris in the past, and rightly so.
"But since the gaffer has come in he recognised the ethos and beliefs of everyone at Newcastle United, which was probably summed up on Monday night by making a very positive substitution at 1-0 down at Everton.
"That's what the fans want to see Newcastle United teams doing. The manager recognises that and that's why they really appreciate the fantastic job he is doing."
Hughton will return to the Sports Direct Arena as manager of Norwich on Sunday afternoon, but Harper insisted there will be no room for sentiment after kick-off: "He did a fantastic job here and I am sure the fans will reflect that by giving him a fantastic ovation on Sunday up until kick-off, and then as soon as kick-off comes they will be desperate for three points.
"I am sure the fans will show their appreciation for Chris before and after the game. He might even get a song during the game if we are 3-0 or 4-0 up!
"It will be great to see Chris and Colin back at the club. But hopefully we will send them home with three points for Newcastle on the board."