Christianity has been introduced into Jaffna, the capital of Northern Province of Sri Lanka, in mid 16th century. Then Jaffna was the capital of a separate political entity called the Kingdom of Jaffna. Initially it was very difficult for Portuguese to undertake any religious activity in Jaffna as the king and the people of Jaffna strongly resisted it. In 1591 Portuguese captured Jaffna and installed a king of their choice and got the right to do religious work in the kingdom. During this period Portuguese priests constructed few churches, mostly temporary structures. However, they were successful in converting Jaffna people to Christianity only when Portuguese took the kingdom directly under their rule in 1620.

Portuguese built several Catholic Churches all over the Jaffna Peninsula. Sketches of some of these churches are found in books written by Dutch priest Baldeus.

Portuguese ruled Jaffna unto 1658. Dutch captured jaffna from them. Dutch who followed Protestantism banned all religious activities of Portuguese who were Catholics. Portuguese churches existed at that time were either converted into the new religion or allowed to become ruins.

Dutch rule in Jaffna lasted about 140 years and they also built several churches in Jaffna, but none of those survived. One of the Dutch churches, which was built within Dutch fort of Jaffna stood there intact till the beginning of 1990s and fell into ruins together with the fort due to heavy fighting around this area.

All the old church buildings in Jaffna at present were built during British rule in Jaffna. British captured Jaffna from Dutch in 1796 and ruled it till 1948. During their period, compared to the previous regimes, the government observed tolerance towards other religions. Several Catholic churches also had been built during this period.