Nagercoil derives its name from the famous old Nagaraja Temple (temple of the serpent king) which is in the central part of town. It has been an important temple for Hindus for centuries as well as a tourist attraction. According to certain accounts, it may once have been a Jain temple, as icons of the Jain Tirthankaras — Mahavira and Parsvanatha — are found on the pillars of the temple.
Nagercoil came under the rule of various kingdoms, notably the Chera, Chola and Pandya kingdoms, Historical records reveal that these kingdoms fought over the control of the fertile area of Nanjilnadu and Kottar, a town mentioned in old Tamil writings and maps of ancient India. Archaeological records also show Jain influences in ancient times.
The modern history of the town is interwoven with the history of Travancore state. The modern town of Nagercoil grew around Kottar, now a locality in the municipal limits. The town came to prominence during and after the reign of Maharaja Marthanda Varma, the king of Travancore, the capital of which was Padmanabhapuram, about 20 km to the north of Nagercoil. The capital was later shifted to Trivandrum, now Thiruvananthapuram, the capital of Kerala state, about 65 km to the north of Nagercoil. In the erstwhile princely state of Travancore, Nagercoil was the second most important town after the capital Trivandrum.
Maharaja Marthanda Varma's successors continued the land, revenue and social reforms he instituted. Although Travancore was considered by many to be a "Hindu" administration, the rulers generally showed religious tolerance and were not hostile to European educators, missionaries and traders. Until the 19th century, the coffers of Travancore were greatly helped by revenues from the trade of pepper and other spices, with the European powers.
Irrigation systems (an excellent system is still found around Nagercoil), dams, roads, schools etc. developed under the administration of the Travancore royals and
