By now Stoke had lost the valuable services of Tom Robertson, Jack Kennedy and Joe Turner while dedicated full-back Jack Eccles made only two appearances and later became club trainer as the team slowly broke up. Only two points were collected from their first eight games and a disjointed Stoke side slipped to the bottom of the table. The situation improved slightly with the arrival of Welsh forward Mart Watkins from Oswestry Town but Stoke were seemingly always tied down to being involved in a relegation dog-fight and that's how it was right up until the final day of the season.
On Good Friday (5 April 1901) Stoke went to Bury and were denied two blatant penalties and lost 3–2. This defeat left Stoke in 17th position, three points and one place above West Bromwich Albion who had three games in hand, while Preston and Wolves were just above them. Stoke's remaining two games were both away - to Wolves and Notts County. Preston ended their season with a home clash with West Brom who were struggling to find any form and looked doomed. Remarkably, Stoke upped their game and won both matches while Preston lost and went down with Albion leaving Stoke safe in 16th place. It had been a tense and difficult season and the club's finances were now in a very precarious state, both manager and chairman recognized this and the club would now look at the local leagues for players.
Unfortunately ace marksman William Maxwell bid farewell to Stoke at the end of the season joining Third Lanark for £250 after scoring 85 goals in 173 games for the "Potters" and he would be sorely missed.
The 1900–01 season saw the introduction of a short lived intermediate round before the first round proper, Stoke beating Glossop 1–0. In the first round Stoke lost 2–1 in a replay to Small Heath after a 1–1 draw at the Victoria Ground.