The church was designed by Father G. Gannon, parish priest of Sea Street. Although the foundation stone was laid by the Archbishop of Colombo, Pierre-Guillaume Marque, on 2 February 1936, construction was not completed until ten years later. It replaced a smaller church to accommodate the increasing number of parishioners in the catholic majority city. It is said to be modeled in Gothic style on the lines of the Reems Cathedral in France. A shadow of this church is seen in the Negombo Lagoon.
This church is one of the many churches in Sri Lanka dedicated to St Sebastian who is considered a martyr in the Catholic Church history. His veneration is particularly celebrated seeking relief from epidemics. A festival called the “Feast of St Sebastian” is held every year here during the month of January. A tali drama narrating the Life of Sebastian used to be enacted here before 1950. Now, “Raja Tunkattuwa”, a Sinhalese language drama about the Three Kings is held here during Christmas.