At the Rajagopalaswamy Kulasekara Perumal Koil, one finds several inscriptions relating to significant contributions made by rulers dating back to the Chozha and Chera period. Rajendra Chozha made big contributions to this temple in the 11th century AD, so much so that this place was referred to as Rajendra Vinnagaram. Later, Chera King Rajasimman donated several pieces of land to this temple. Jaya Varma Chozha Pandya, as well as Nayak kings, also made contributions to the Mannar Koil. There are also interesting inscriptions on the floor of the temple right at the entrance.

Kulasekara Azhvaar, who was born in Thiruvanjikalam went on to become a Chera King. During his early years, he defeated Chozha and Pandya kings and was a dominant force. However, his devotion to Lord Vishnu led him to renounce power and to a path singing praise of the Vaishnavite Lord. After trips to several Vishnu temples, Kulasekara Azhvaar finally reached Mannar Koil, where he was taken in by the beauty of Vedanarayanan, in whom he saw the Lord Ranganatha of Srirangam. Like Srirangam, Mannar Koil too is surrounded by two rivers on either side -Thamirabarani River on the Southern side and Gadananathi River on the Northern side. Staying here at Mannar Koil for over 30 years, Kulasekara Azhvaar undertook daily pooja of Lord Rama, who was his abhisheka deity and finally attained moksha at this place. To this day, one finds the idols of this Abhisheka Moorthy at this temple. In recognition of his efforts here at Mannar Koil, this temple has come to be known as Kulasekara Perumal Koil, the only historical Perumal Koil to be directly named as an Azhvaar Perumal Koil. One also finds the Kulasekara Azhvaar Sannidhi with the Holy Flag Post (Kodi Maram) dedicated to him, a speciality (for Azhvaars) not seen in any other Perumal Koil.