The season was the most successful yet, with St. Mary's claiming the Southern League title for the first time and reaching the Second Round Proper of the FA Cup.

The team started the league season with a run of nine consecutive victories, including defeating Sheppey United 6–1, New Brompton 8–3 and Reading 6–0 (all at home).

The championship was secured only in the penultimate match of the season on 14 April, a 2–1 victory over bottom club, Wolverton, with the two points earned putting St. Mary's out of the reach of their nearest rivals, Millwall.

Millwall scored first early in the match, but Southampton fought back to equalise with a "brilliant shot" from Joe Turner following one of his "mesmerising dashes down the wing".

[2] As team captain, Farrell received the Championship shield from Dr. Russell Bencraft, who was both president of the League and of the club, at a ceremony in the Artillery Drill Hall in Southampton.

Several thousand travelled to the Isle of Wight to see the "Saints" comprehensively outplay Cowes, with Robert Buchanan, Jack Farrell and Joe Turner each scoring twice in a 6–0 victory.

St. Mary's had to travel again in the next round, to visit Elm Park; on arriving at the stadium, the team found the pitch waterlogged.

McMinn lodged a protest with the referee, who declared the pitch playable so the match went ahead with the Saints winning 4–1.

This put Southampton through to the First Round Proper for the third consecutive season, where they met Derbyshire club, Heanor Town.

[8] At this time, the only other local professional football club was Freemantle, who had ended the 1896–97 season in a crisis, having been denied promotion to the Southern League First Division after they had used a player whose transfer had not been registered.

[9] At St. Mary's meanwhile, a sub-committee had been established to look into playing arrangements for the 1897–98 season, as the cost of hiring the County Ground from the Cricket club was prohibitive.

Although delegations from both sides met to discuss the proposals, there was strong opposition and after much deliberation the St Mary's committee decided not to proceed.

"[10] At a further meeting at the offices of the club's lawyers on 16 July, arrangements were made for the issue of shares, with Tankerville Chamberlayne being invited on to the board.

Horne (dairyman), W. Newnham (law clerk), Edward Brown (butcher) and Charles Robson (mineral water merchant and wicket-keeper for Hampshire, who had been the St. Mary's club secretary in 1895–96) had been added to the list of directors.