Rathnapuram had some 160 years earlier a small chapel dedicated to St. Francis Xavier. It was a substation to the Cathedral parish. In 1962, Rev. Fr. Maria Alphonse Kagoo built a school building where the chapel was standing.
Bishop Thomas Fernando wanted to have a parish in Rathnapuram and so he bought the land around the school building. When Rev. Fr. Lambert Miranda was the parish priest of Cathedral in 1973 Bishop Ambrose Mathalaimuthu laid the foundation for a new Church. When Rev. Msgr. Stephendas was the parish priest of Cathedral he built the altar and sacristy of the Church. In 1984 Rev. Fr. Job de Rose completed the Church construction. On 20th December 1986 the Church was blessed.
In 1990 Rev. Fr. Gerald was appointed priest in charge of Rathnapuram in order to make arrangements for errecting Rathnapuram into a parish. Rev. Msgr. Lambert Miranda, the Vicar General, laid the foundation for a presbytery on 24th June 1992. Rathnapuram was elevated into a parish and Rev. Fr. S. Gabriel was appointed as the first parish priest. Rev. Fr. Job De Rose had a second inning as parish priest and he put up the belfry and the Mandapam in front of the Church.