The history of Tirunelveli was researched by Robert Caldwell (1814–91), a Christian missionary who visited the area. Tirunelveli was under the rule of Pandya kings as their secondary capital; Madurai was the empire's primary capital. The Pandya dynasty in the region dates to several centuries before the Christian era from inscriptions by Ashoka (304–232 BCE) and mention in the Mahavamsa, the Brihat-Samhita and the writings of Megasthenes (350–290 CE). The province came under the rule of Cholas under Rajendra Chola I in 1064 CE; however, it is unclear whether he conquered the region or obtained it voluntarily. Tirunelveli remained under control of the Cholas until the early 13th century, when the second Pandyan empire was established with Madurai as its capital.
The Nellaiappar temple was the royal shrine of the later Pandyas during the 13th and 14th centuries, and the city benefited from dams constructed with royal patronage during the period. After the death of Kulasekara Pandian (1268–1308), the region was occupied by Vijayangara rulers and Marava chieftans (palayakarars, or poligars) during the 16th century. The Maravars occupied the western foothills and the Telugas, and the Kannadigas settled in the black-soil-rich eastern portion. Tirunelveli was the subsidiary capital of the Madurai Nayaks; under Viswanatha Nayak (1529–64), the city was rebuilt about 1560. Inscriptions from the Nellaiappar temple indicate generous contributions to the temple. Nayak rule ended in 1736, and the region was captured by Chanda Sahib (1740–1754), Arcot Nawab and Muhammed Yusuf Khan (1725–1764) during the mid-18th century.
In 1743 Nizam-ul-mulk, lieutenant of the Deccan Plateau, displaced most of the Marathas from the region and Tirunelveli came under the rule of the Nawabs of Arcot. The original power lay in the hands of the polygars, who were originally military chiefs of the Nayaks. The city was the chief commercial town during the Nawab and Nayak era
