Ptolemy refers to Nagapattinam as Nikam and mentions it as one of the most important trade centres of the ancient Tamil country. Nagapattinam was a Buddhist centre from 8th century CE. In 11th century CE, Chudamani Vihara, a Buddhist vihara (monastery) was built by Javanese king Sri Vijaya Soolamanivarman with the patronage of Raja Raja Chola. Buddhism flourished until 15th century CE and the buildings of the vihara survived until 18th century. In Chola's Empire, Nagapattinam was the prominent port of Cholas and Cholas used this port not only for trade but also as conquering gateway to the east. This town still has traces of Saiva temples that were built by Cholas.
Nagapattinam was referred to by early writers and the Portuguese as "the city of Coromandel". In early 16th century the Portuguese start commercial contacts with the town; in 1554 they establish a commercial centre. In 1657 the Dutch occupied the town, taking it from the Portuguese to become their chief possession in India. In 1676, when the Maratha prince Venkaji had established himself at Tanjore, the grant of Negapatam to the Dutch was confirmed.
During the 18th century, two naval battles between British and French fleets were fought off the coast of Negapatam, as it was then known; the Battle of Negapatam (1758) as part of the Seven Years War, and the Battle of Negapatam (1782) as part of the American Revolutionary War. The town was taken by the British from the Dutch (who were loosely allied with the American revolutionaries) in 1781, then by the French admiral Pierre André de Suffren de Saint Tropez. On January, 20th Nagapatnam was given to the English by Charles Gravier, comte de Vergennes. From 1799 to 1845 it was the headquarters of Tanjore district.
Nagapattinam was one of the regions severely affected by the tsunami which followed the 2004 Indian Ocean earthquake.