The 1998–99 season was Port Vale's 87th season of football in the Football League, and fifth successive season in the First Division. It was the end of an era for the club, as manager of sixteen years John Rudge was sacked in January, and was replaced by Brian Horton. As a testament to the upheaval at the club, a club record 43 players turned out for the Vale in the league over the course of the season. The Vale just avoided relegation on goals scored, despite suffering a final day defeat to Bury, who were relegated having scored ten fewer goals. Liverpool knocked them out of the FA Cup at the Third Round, and Vale were also knocked out of the League Cup by fourth tier Chester City in the First Round. The sacking of Rudge spoiled what was supposed to be a happy season for Vale fans, as Vale competed in a division above rivals Stoke City for only the fourth time.

The pre-season saw John Rudge splash out £300,000 on Bristol Rovers forward Peter Beadle and £100,000 on Scunthorpe United defender Michael Walsh. He also signed Dave Barnett (Dunfermline Athletic); Brian McGlinchey and Paul Beesley (Manchester City); and John McQuade (Hamilton Academical) on free transfers. Stéphane Pounewatchy also became the first French player to play for the club when he was signed on a monthly contract from Dundee. Scott Mean was loaned to the club by West Ham United, though he went on to sustain a knee injury during his spell that would damage his career. Also Andy Clarke was signed on loan from Wimbledon.

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