Around 1790, the Archbishop of Goa at the request of Dom Manuel Noronha, a Portuguese officer working in the Peshwa's army, sent Fr. Vincent Joaquim Menezes to minister to the Catholics working in the army of Peshwas. Fr. Menezes resided and said Mass in the house of Dom Noronha. In 1794, with the contribution of the Catholics in the army, a small chapel was built at Nana Peth on a plot offered by the Peshwa. The first Mass was celebrated in this chapel on Christmas day. These were the beginning of the Church of the Immaculate Conception, commonly known as the City Church. Around 1800 the Vicar Apostolic of Bombay started sending his priests to minister to the Catholics in the Scindia's army but he stopped this about 1804. In 1835 Fr. Britto, a priest from Goa working under the Vicar Apostolic acted as Military Chaplain in a chapel built at Right Flank Lines, Wanowrie. The Neo-Gothic cathedral was built in 1850 mainly to cater the Irish Catholic soldiers and other Catholics settled in Wanwadi and nearby areas. Earlier, mass was celebrated for the troops, who were mainly Irish and other Catholics in the chapel at the end of Right Flank Lines in Wanwadi. Bishop Anastasius Hartmann OFM Cap., the Apostolic Vicar of Bombay and Poona, wanted to have a better place of worship, and so he co-opted Fr. James Carry, an Irish diocesan priest from the Madras Mission, as a chaplain in Poona in 1849. Fr. Carry immediately drew up plans to erect a new chapel.
At the request of the bishop, the government allotted land. The chapel was built with contributions from people and from the soldiers, who contributed a month's salary. On 8 December 1850, the first mass was celebrated in the new chapel, which is now St. Patrick's Cathedral. The Diocese of Poona was created in 1886 and Jesuit missionary Bernard Beider Linden was appointed the first bishop. Thus, St. Patrick's Church became St. Patrick's Cathedral in 1887.
On 15 July 1984, the roof of the cathedral collapsed. With donations from benefactors, the cathedral was rebuilt with a new curved vault roof designed by architect Charles Correa in place of the old pointed roof. The re-dedication of St. Patrick's Cathedral was held on 22 October 1987. Eventually, the cathedral was again in need of repairs with the passage of time. Major renovation, repairs and redecoration of the cathedral was from 2009 to 2010, three of the highlights of which were a new backdrop to the sanctuary wall with a mosaic of the Risen Christ, 16 unique stained glass panels of the life of Jesus and a skylight above the altar depicting the Holy Spirit in stained glass.