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 rivalsStoke City for only the fourth time.
The season started poorly with three defeats, Lee Hughes scoring a hat-trick for West Bromwich Albion to finish this run off. Two wins opened the month of September, though the month ended with former-Valiant Lee Mills scoring a brace for Bradford City in a 4–0 win over Vale at Valley Parade. In October, Derek McGill signed from Queens Park Rangers, though he would move on to Hamilton Academical later in the year. On 29 October, Gareth Ainsworth became Vale's biggest ever transfer as he was sold to Wimbledon for £2 million. In November, Robin Berntsen became the first Norwegian to play for the Vale when he arrived on loan from Tromsø IL. In addition to this French forward Christophe Horlaville joined on loan from Le Havre, and Des Lyttle also arrived on loan from Nottingham Forest. After winning the first four games in October, Vale then went on a streak of twelve defeats in fifteen games, though the sole victory of this run, a 1–0 win over Bury on 19 December, would prove to be crucial at the end of the season. The win was not enough for Rudge, who would get the sack in January after he made his final two signings: Trinidadian midfielder Tony Rougier from Hibernian for £175,000, and young striker Marcus Bent from Crystal Palace for a £375,000 fee. After Rudge was sacked by Chairman Bill Bell, highly distressed fans formed a "flat cap protest" (Rudge's headwear of choice) against the decision. Offered the role of Director of Football at the club, he instead took up the same position at rivalsStoke City. To replace him, Bell appointed experienced manager and former Vale player Brian Horton.
They finished in 21st position with 47 points, ahead of Bury on goals scored, but behind both Portsmouth and Queens Park Rangers on goals scored. Had the goals difference rule been in effect then Vale would have been relegated instead of Bury. Crewe Alexandra finished three places and one position higher than the Vale. Vale suffered 25 defeats, more than any other club in the league, and only Grimsby and Bury had scored fewer goals. Player of the Year Martin Foyle was the club's top-scorer with nine goals, representing the lowest total tally for the club's top-scorer since 1964–65. Only Paul Musselwhite and Allen Tankard managed to hit forty appearances, as a club record 43 players managed to turn out for the club throughout the season.