The club entered, and won, the Hampshire Junior Cup in its inaugural year, thus laying the foundation for success over the next two decades.

Two years after being founded, the club began to embrace professionalism and move away from its roots, gradually severing its connection to St. Mary's Church to become a more secular organisation, eventually dropping references to the Young Men's Association becoming simply St. Mary's Football Club and, at the same time, acquiring the nickname, "the Saints" which remains to the present day.

[4] As secretary of the Hampshire County Cricket Club, Bencraft was also a colleague of Col. James Fellowes, who was an assistant to the Director-General of the Ordnance Survey.

[7] A photograph taken after their victory in the Hampshire Junior Cup in March 1888 shows the sashes worn from either shoulder in a rather haphazard fashion.

The newly formed Hampshire Football Association held its first meeting on 20 April at the Spartan Club in Southampton High Street when St. Mary's were represented by Messrs. Varley and Bromley.

[8] This problem did not arise with the first round match, when the club were drawn to play at Totton who had only been formed the year before but had the use of a field within the grounds of a private estate at South Testwood Park.

A. Fry ran the whole length of the field before landing the ball directly in front of his captain, just a few yards out – Bromley simply couldn't miss".

The "Arabs" were a strong side and took the lead, after which Carter and Muir in defence ("certainly the best on the field" according to the Southampton Times) prevented them from playing other than by shots from distance.

The equaliser came from McDonald before, late in the second-half, Bromley "dribbled in great style down the field, and put the ball through for St. Mary's", thus securing a place in the final.

[5] St. Mary's fell behind early in the game and were 2–0 down at half-time but fought back to draw level at 2–2, with goals from Warn and Ned Bromley who unleashed a "splendid shot" with three minutes left to play.

In the absence of goal nets, the ball had crossed the line, but the Harriers "kicked off from the six yards' mark and no claim was made by St. Mary's for the point.

[9][11] The replay was played two weeks later, again at the County Ground in front of a crowd of "over 500 people, exclusive of the ladies who, bless 'em, are admitted free.

The final match of the season was played at the Antelope Ground on 14 April 1888 against Woolston Works who had won the inaugural Hampshire Senior Cup.

The home side were victorious by three goals to nil; the Bournemouth Guardian report on the match summed up the clubs' season: Both teams have had a wonderfully good time of it on the whole and the people of Southampton ought to feel proud of their football population.

The recruitment of players such as George Carter, who had been signed for his abilities as a footballer rather than a Sunday School teacher, indicated a shift away from this policy.