They ended the season third in the Southern League, but reached the final of the FA Cup, thus becoming the first southern professional side to do so, and the first side from south of the midlands since 1883. In the final, they played badly as a result of divisions amongst the players and lost 4–0 to Bury.

Having won the Southern League title in each of the three previous seasons, Southampton were now considered to be the best football team in England outside The Football League. The club had considered applying to join the league but decided that, because of their location on the south coast, the cost of travelling would be prohibitive. The popular boys' newspaper, Chums featured the club in their October 1899 edition:

The Southampton club is the surprise packet of the football world. No team can boast of having fought their way to the front with such lightning-like rapidity as the champions of the South and, if the opinion of experienced judges are worth anything, the Southampton men have absolutely no superiors. It is true that they do not engage in first League duels, but the reason they do not do so is not that they consider they stand no chance of achieving premier honours, but that the departure would not pay them. There are no League clubs in the South, the consequence being that if Southampton were to enter for the competition, about half their time would be spent in travelling to the North and back — a proceeding that would soon land them high and dry in Bankruptcy Court.

With the club £1,000 in debt and in an attempt to ensure success on the pitch, the directors had recruited several top-class players on substantial wages. In order to meet these, the cost of entry to home matches was doubled from sixpence to a shilling. The opening Southern League match was attended by a meeting of "anti-bobs" in Milton Road; "after [their] grievances had been aired, the participants therein wended their way to other haunts than the football field". As a result, the attendance for the match against New Brompton was "disappointingly small" with "barely two thousand people present". Explaining the decision to double the price of admission, the secretary Mr. Arnfield told the Football Echo

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