The region around Kumbakonam was inhabited as early as the Sangam Age (3rd century BC to 3rd century AD). The present-day Kumbakonam is believed to be the site of the ancient town of Kudavayil where the Early Chola king Karikala held his court. Some scholars identify Kumbakonam as the site of the fabled prison of Kudavayir-kottam where the Chera king Kanaikkal Irumporai was imprisoned by the Early Chola king Kocengannan. Kumbakonam is identified with the town of Malaikūrram which had served as the Chola capital as early as the 7th century and with the town of Solamaligai which had also served as a Chola capital. According to the Sinnamanur plates, Kumbakonam was the site of a battle between the Pallava king Sri Vallabha and the then Pandya king in 859 and between the Pandya king Srimara Pandya and a confederacy of the Cholas and Gangas.
Kumbakonam came into limelight during the rule of the Medieval Cholas who ruled from the 9th century to the 12th century. The town of Pazhaiyaarai, 8 km (5.0 mi) from Kumbakonam was the capital of the Chola Empire in the 9th century.
Following the decline of the Chola kingdom, Kumbakonam was conquered by the Pandyas in 1290. Following the demise of the Pandya kingdom in the 14th century, Kumbakonam was conquered by the Vijayanagar Empire. Krishnadevaraya (1509–29), the emperor of Vijayanagara visited the town in 1524 and is believed to have bathed in the famous Mahamaham tank during the Mahamaham festival. Kumbakonam was ruled by the Madurai Nayaks and the Thanjavur Nayaks from 1535 to 1673 when it fell to the Marathas. Each of these foreign dynasties had a considerable impact on the demographics and culture of the region. When the Vijayanagar Empire fell in 1565, there was a mass influx of poets, musicians and cultural artists from the kingdom.
According to the chronicles of the Hindu monastic institution, the Kanchi matha, the matha was temporarily transferred to Kumbakonam in the 1780s following an invasion of Kanchipuram by Hyder Ali of Mysore. When Tipu Sultan invaded the east coast of South India in 1784, Kumbakonam bore the brunt of his invasion. The produce fell sharply and the economy collapsed. Kumbakonam did not recover from the calamity till the beginning of the 19th century.
Kumbakonam was eventually ceded to the British East India Company in 1799 by the Thanjavur Maratha ruler Serfoji II (1777 -1832) and reached the zenith of its prosperity in the late 19th and early 20th century when it emerged as an important center of Brahminism, Hindu religion and European education in the Madras Presidency. The opening of the Suez Canal in 1869 fostered trade contacts with the United Kingdom. In 1877, railway lines were completed linking Kumbakonam with the ports of Madras, Tuticorin and Nagapattinam. The Tanjore district court was established in Kumbakonam in 1806 and functioned from 1806 to 1863.
Kumbakonam continued to grow even after India’s independence though it fell behind the nearby town of Thanjavur in terms of population and administrative importance.