The twin-spired neo-gothic structure was built on the site of an old Portuguese church by a French priest, Father Farve in 1856 in honor of St. Francis Xavier, a prominent 16th-century Catholic missionary also known as 'Apostle of the East'. The church is located on Jalan Laksamana, the finishing touches were completed in 1859 by Father Allard with current presbytery built in 1874.
Currently, St. Francis Xavier's Church still serves its function as a Catholic church with regular mass services being held from time to time. The church's building now leans slightly to the left.