The Pandya King Kulasekaran built a temple, which would later be known as the Meenakshi Temple, and created a lotus shaped city around the temple. Legend has it that on the day the city was to be named, as Lord Shiva blessed the land and its people, divine nectar was showered on the city from his matted locks. This city was henceforth known as Madhurapuri, meaning "The Land of Divine Nectar". According to a different theory, the name Madurai is actually a transformation of the Tamil word "Marudhai" (?????), which means a fertile agricultural land with alluvial soil. Many natives continue to refer to the city as Marudhai. The city has been called the "Athens of the East" because of its great architecture and meticulous planning, comparable to that of the Greek capital.

Madurai is Tamil Nadu's oldest city and one of India's oldest cities, with a history dating back to the Sangam period of the pre-Christian era. It was home to the ancient Tamil Sangam (The Academy of Tamil Learning), the literary conclave that produced the first Tamil epic Silappathikaaram and other masterpieces of Tamil literature. Megasthenes, the ancient Greek diplomat and envoy to India in 3rd century BC, had written in glowing terms about it in Indica, his celebrated account on India. But Madurai was to reach its heights of glory in the hands of the Cholas, and finally the Pandyas in the 13th century. After all, the Pandyas were the ones that made the city their capital, and built the Meenakshi Temple, which has always been the greatest attraction of the city. The city flourished under Pandya rule when it was a major trading hub with trading contacts with Greece, Rome, and Middle Eastern countries.

It was a fall from eternal glory to deep abyss for Madurai when the Tamil Kingdoms disintegrated, and its wealth was plundered by the ravaging armies of Delhi's Muslim Rulers. In 1311, it was raided by Malik Kafur, the general of Alauddin Khilji of Delhi. In 1371, the Muslim rule of Madurai was put to an end by the Vijayanagar Rulers who annexed the city to their Kingdom. The Vijayanagar Rulers had the practice of appointing Governors to administer their distant territories. The Governors appointed to rule Madurai were called Nayaks (or Naiks), and it was during their rule that the city regained some of its past glory. When the Vijayanagar empire collapsed in 1565, the Nayaks proclaimed themselves rulers of the territories they governed.

The Nayak Rulers, Thirumalai Nayak, in particular, gave a good boost to the architectural legacy of the city by creating new structures and expanding the existing landmarks in and around the city. The Raja Gopuram (The Main Tower) of the Meenakshi Temple, Puthu Mandapam (The New Mansion) and the Thirumalai Nayak Palace are living examples of his unparalleled contribution to the city's architecture.

On Thirumalai Nayak's death in 1659, the kingdom began to break up. His successors were weak rulers and invasions of Madurai recommenced. Shivaji Bhonsle, the great Maratha Ruler, invaded the south; and so did Chikka Deva Raya of Mysore and other Muslim Rulers, resulting in chaos and instability all around. The one redeeming feature of this period of confusion and anarchy was the regency of Rani Mangammal, who stood up against these invasions. Though her rule lasted no more than two decades, she will forever be cherished by the people of Madurai for the prudence, determination and courage she exhibited during a particularly troublesome period, with very little support from outside.

Madurai soon started slipping into the hands of the British East India Company. By 1801, the whole of Madurai district, which then was made up of Dindigul, Palani, Kodaikkanal, Ramanathapuram and Sivagangai was brought under the control of British East India Company.