In 1838 Bishop Patric Griffith arrived at the Cape from Ireland as the first resident Bishop. From then on a priest would occasionally go to Simon's Town to minister to the biggest concentration of Catholics in the area outside Cape Town. It is recorded that Mass was celebrated on the convict ship "Neptune" in Simon's Town on 11 February 1850.

In 1850 the first Catholic chapel was built with Rev.Mr. Kiernan as the resident priest. A deed of transfer "for a piece of ground situated in the vicinity and to the eastward of Simon's Town for the purpose of erecting a chapel, a house for a clergyman and a school for religious instruction thereon", had previously been granted to initiate this construction. The original chapel was later used as a classroom in a school which Bishop Rooney had built adjoining the chapel. Miss Aggar was the first principal.

The new church was built of stone from a local quarry. The builder was Mr Patrick Martin whose face is portrayed in the stained-glass window dedicated to St Patrick, which Mr Martin presented to the church. The church was designed by the parish priest Father John Rooney. The Bishop insisted that it cost no more than 650 Pounds (R1300)!. To raise money, Father Rooney opened a subscription list and funds began to trickle in. One entry read: "Captain and men of the flagship Boadicea" - L5-18-4d; another "Captain Andoe and men of the Orontes" - L2-13-6d; the Commander-in-Chief, Rear-Admiral Salmon, gave two Pounds. Several donations were only two shillings, most no more than five; but it all added up to build the church as it stands today.

The close links between the Church and the Navy were strengthened by the appointment of two Catholic Commanders-in-Chief, Vice-Admiral Charlton and his successon Vice-Admiral Fitzherbert. During the former's command Lady Charlton, assisted by her butler, took charge of the Sacristy. In 1869 Bishop Leonard had remarked in his diary that Commodore Dowell offered at his the disposal "The Admiralty House at Simon's Bay" whenever he visited the area.

The church bell, which bears the date 1871, was cast in the Dockyard for Bishop Rooney. By June 1887 the Catholic population of Simon's Town was 64 with 26 children at the school. The priest commented, "much drunkeness and immorality as usual in a seaport town. Besides the civilian congregation there has been an number of soldiers and sailors attending church here. The number has varied from 6 to 58!"

In June 1903 the annual report gives the permanent Catholic population as 184. "The numerical increase in the congregation is due to a considerable number of Italian workmen at the Selborne Dock Extension works in this town. Very few of these men come even to Mass on Sundays. They contribute nothing to the upkeep of the mission."