From 1590, Portuguese merchants and Catholic missionaries were active within the Jaffna kingdom.
Impetus for a permanent fortified settlement happened only after 1619, when the expeditionary forces of the Portuguese Empire led by Filipe de Oliveira captured Cankili II, the last native king.
Residents of Jaffna city along with the rest of Tamil population of Sri Lanka were in the fore front of the political mobilisation behind Tamil nationalist parties.
After the Tamil conference incident in 1974, the then mayor of Jaffna Alfred Duraiappah was assassinated by the leader of rebel LTTE, Velupillai Prabhakaran in 1975.
During the British colonial period, almost all the schools that eventually played role in the high literacy achievement of the Jaffna residents were built by missionaries belonging to American Ceylon Mission, Weslyan Methodist Mission, Saivite reformer Arumuka Navalar and others.
Bombardment from air and land of the city led to damage to civic and civilian properties, death and injury to civilians and destruction the economic potential of the city.It also has number of commercial institutions, minor industrial units, banks, hotels and other government institutions.It is home to many historical sites such as the popular Jaffna library that was burnt down and rebuilt and the Jaffna fort rebuilt during the Dutch colonial period. The origin of the name can be traced to a legend about the town's etymology.They also built Presbyterian churches and government buildings, most which survived until the 1980s, but suffered damage or destruction during the subsequent civil war.Britain maintained many of the Dutch mercantile, religious, and taxation policies.