Having initially taken over on a temporary basis, by the beginning of the 2001-02 season the permanent nature of manager Willie Hume's position had been confirmed. John Reid continued as player/assistant manager, with Jack Diamond, who had returned to the club from Arniston Rangers the previous season, now combining his playing role with that of coach. Despite reaching the quarter finals of the Image Printers Cup, the semi final of the League Cup and the final of the King Cup the previous season, in the Premier Division Vale finished only a point away from a relegation place. A major priority for the men in charge therefore, was to strengthen a squad which had been severely hampered by injuries and suspensions during it's hectic end of season schedule. A major blow was the loss of the fruitful strike duo of Peter Moffatt and Scott Dyett, who had between them claimed over a hundred goals during the previous three seasons. To fill the gap, ex-Edinburgh City and Peebles Rovers striker John Coogan was recruited, along with Craig Ford from Spartans, Darren Lockhart from Lothian Thistle and Earlston twins Craig & Gary Lothian from Berwick Rangers Under-18 side.

Pre-season was little more than a stroll in the park, with the first game against Newtongrange Star Under-21's finishing 6-2 in favour of Vale. Amateur sides Danderhall and Earlston Rhymers were swept aside before Vale's stiffest pre-season test - another meeting with Kirriemuir Thistle which this time ended in a draw.

Vale got their league campaign off to a winning start at Victoria Park against Edinburgh City courtesy of a 79th minute strike from Lindsay Rathie who had replaced John Coogan only minutes earlier. The first away fixture came at Netherdale, against a Gala Fairydean side who had got off to a bad start under new boss, ex-Dundee United star John Clark. Vale raced into a two-goal lead through Rathie and Phil Johnson and although they let the home side back into the game when Clark - who was playing for as well as managing Fairydean - pulled one back, held out for three points.

In the Scottish Qualifying Cup, South of Scotland League side Wigtown & Bladnoch were drawn at home in the Preliminary Round and Phil Johnson scored four as Vale ran out comfortable 7-1 winners to set up a First Round meeting with Gala Fairydean. Previously before big cup-ties, Stuart Robertson liked to get the players in early to have a pre-match meal together and foster squad unity, but Willie Hume tried a different approach, aiming to prevent potential nerves by treating the build up just like any other game. A bad start to the match by Vale contributed to the final result, a 2-0 victory sending Fairydean into the next round and eventually into the Scottish Cup proper where they progressed to the Third Round, recording a famous victory over Scottish League side Stirling Albion along the way.

In the First Round of the Image Printers Cup, Vale overcame Edinburgh Athletic despite a battling performance by the capital side, to set up a Second Round derby clash with Peebles Rovers. Vale had to withstand another spirited performance at Whitestone Park by their opponents, who were left livid when a late winner by Jamie Yuill was allowed to stand despite appearing to be offside. Quite often these things can even themselves out and it was Vale's turn to cry foul in their Third Round tie at home against Whitehill Welfare. The clubs previous meeting had contained more than it's fair share of drama and controversy and on this occasion a John Coogan penalty opened the scoring before Whitehill equalised with a Scott Hunter header. Vale felt they should have had a late penalty when John Coogan was held back when clear on goal, but the referee waved play on and Whitehill broke quickly upfield for Steven O'Donnell to net the winner. The final moments of the match saw tempers fraying and a red card for visiting midfielder Willie Bennett, with Whitehill manager Dave Smith having to escort his player from the field before being sent from the dugout himself.

In the Premier Division, Willie Hume had set his sights on a top three finish and a magnificent shot into the roof of the net from 30 yards by Danny O'Donnell brought victory at defending champions Annan Athletic, but Vale surrendered a two-goal lead to draw at Craigroyston and needed an injury time equaliser to salvage a point against Pencaitland & Ormiston. A Jamie Yuill diving header in the 15th minute completed a double over Edinburgh City at the Commonwealth Stadium, however for the second year running Vale crumbled in embarassing fashion at home against Threave Rovers.

A spell of bad weather at the turn of the year decimated the fixture card and the league meeting with Edinburgh University was switched to the capital to allow Vale their only action during the month of February. Even training was affected, with sessions cancelled or curtailed due to weather conditions and the spell of inactivity saw Vale slump to fourth from bottom of the league.

Vale suffered another cup defeat at the hands of Gala Fairydean in the King Cup, thanks to an Ian Baillie goal two minutes into the second half at Netherdale. The game was more notable however, for an altercation between Fairydean player/manager John Clark and Vale defender Danny O'Donnell, after the former's alleged use of an elbow. Afterwards Clark defended himself in the press, calling it, "a man's game," and criticising O'Donnell for refusing to shake hands at the final whistle before turning on the Vale manager, concerning comments he had made about the conduct of some Gala players.

In March, former Vale boss Stuart Robertson made his first return to Victoria Park since his resignation in a league fixture against his Coldstream side. The teams had previously drawn in an earlier fixture at Home Park and the return saw the same outcome, thanks to a late equaliser by Streamers' Paul Wilson. Vale had the best of the game but were denied by a string of top drawer saves by a young goalkeeper on trial from Easthouses Under-21's called Iain Gordon, who would later link up with Robertson again, when he joined Vale in 2004.

Snow and rain was still causing a fixture backlog, but Manager Willie Hume suffered problems of his own while taking part in bounce games in training. Firstly a challenge from Robbie Clark left the gaffer with a bruised rib, then a couple of weeks later an accidental collision with Euan Hoy left him with a broken rib and bruised kidney. "Maybe they think I'm going to pick myself so they're trying to keep me out the team," sighed Hume.

After falling at the first hurdle of the League Cup to Whitehill Welfare, Vale embarked on the final fixtures of their league campaign, and an interesting encounter with Gala Fairydean mid-April. A John Martin double sealed the win for Fairydean and despite there not being a single bad challenge during the 90 minutes referee Robert Solley saw fit to book John Coogan, Jamie Yuill and Darren Lockhart along with Fairydean's Clark, Martin, Robert Findlay, Stuart Brown and Steven Sweeney. In the build up to the game, Willie Hume had played down talk of residual bad feeling after the King Cup tie, but resentment obviously still ran high, with angry scenes at the end of the game as John Clark insisted that his players proceeded immediately to the dressing rooms without shaking the hands of their opponents.

Barry Joyce challenges for the ball in the league match against Gala Fairydean - a game that ended in controversy.

Victories over the two relegated teams saw Vale finish level on points with Threave Rovers, but with an inferior goal difference, and only three points behind their third place target, prompting some wistful reflection on what might have been.

There was a boost at the end of the season, when top scorer Phil Johnson was invited to play for a Scottish non-league representative side in the end of season Unibond Four Nations Tournament against similar sides from England, Wales and Northern Ireland. He scored in a warm-up game against Queens Park and went on to appear in all three tournament games where Scotland unfortunately failed to register a win, but the prestige of being selected to play at international level reflected well on player and club. There was disappointment though for defender Danny O'Donnell when he had to withdraw from the trial squad due to a foot injury.