The 1999–2000 season was Port Vale's 88th season of football in the Football League, and sixth successive season in the First Division. Vale suffered relegation in 23rd place, some thirteen points adrift of safety. They also exited the FA Cup at the Third Round, and were knocked out of the League Cup at the First Round by fourth tier Chester City for the second consecutive season. The club spent nothing on transfers, but sold young players for some £1.5 million – despite this the club was heading towards bankruptcy. The club continued to gain one generation of players at the expense of the successful '90s generation; Martin Foyle, Paul Musselwhite and Ian Bogie departing, with fresh talent such as Micky Cummins and Mark Goodlad arriving in their place.
The season started with a goalless draw at Ewood Park with Blackburn Rovers, but soon went downhill with two defeats. Vale then entered inconsistent form, winning three and losing three in a run of six games. However just two points from seven October games indicated Vale's future. Also in the month, striker Marcus Bent, signed by John Rudge nine months earlier for £375,000, was sold to Sheffield United for a bargain £300,000, and was later sold on by the "Blades" for a £1.7 million profit. The club set a record on 5 September, when just 3,737 turned up to see a 3–0 win over Grimsby Town – a division record low for a television match. The Vale ended the year in solid form, unbeaten in seven games, despite just two victories (over rivals Crewe Alexandra and against Sheffield United at Bramall Lane). In December, Carl Griffiths was sold back to former club Leyton Orient for £100,000.
They finished in 23rd place with 36 points, a massive thirteen points away from the safety of West Bromwich Albion, and only ahead of Swindon Town on goals scored. With just seven victories, they had the fewest wins in the division. Tony Rougier only needed nine goals in all competitions to become the club's top-scorer. The relegation meant that Brian Horton lost his 'proud record' of never being relegated as a player or as a manager.
In the League Cup, for the second successive season Third DivisionChester City knocked the Vale out at the First Round. In the 2–1 defeat at the Deva Stadium both sides finished the game with ten men, and as the return leg was a 4–4 draw, Chester achieved a 6–5 aggregate win.