It was another poor season for Stoke, as they again finished bottom of the Football League but this time they failed to gain re-election and their place was taken by Sunderland and Stoke joined the Football Alliance for the following season. Stoke's worst league and FA Cup defeat came during the 1889–90 season, a 10–0 reverse against Preston North End and an 8–0 cup defeat to Wolverhampton Wanderers. Stoke won just three matches all season and picked up just ten points making it the club's worst performance in league football.

After finishing bottom of the league last season Stoke failed to improve a great deal in the 1889–90 season and again took the wooden spoon. They were humiliated 10–0 in the second match of the season away at Preston North End where all the goals were scored by Scottish internationals as Stoke suffered their worst league defeat. Stoke also lost 8–0 away to both Everton and Blackburn Rovers and they also suffered a 6–1 reverse against Aston Villa. Stoke were awful throughout the season and went on a ten match losing streak stretching from 19 October 1889 to 4 January 1890. In a tough home fixture against Burnley just before Christmas, Bob McCormick, the Stoke inside-right, badly injured his collar bone in a challenge with the Burnley full-back and at the end of the match and the fans invaded the pitch and confronted the "Clarets" defender. Stoke won the match 2–1 but Burnley lodged an appeal claiming their players had been intimidated. The League decided in Burnley's favour and ordered the match to be replayed, this time Burnley won 4–3.

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