Like every temple in Kerala, Mannarasala Sree Nagaraja Kshetram too is home of many festivals. Maha Shivaratri, Kumbham, Kanni and Thulam Ayilyam are the most important festivals at Mannarasala.

The most celebrated festival at Mannarassala is the Ayilyam in the Malayalam month of Thulam. It is known the world over as Mannarasala Ayilyam. How Thulam Ayilyam got prominence is an interesting story. It was a regular custom for the Maharaja of Travancore to visit this temple on Ayilyam day in Kanni. On one occasion, the Maharaja could not reach the temple as usual and had to postpone the visit to the Ayilyam day in Thulam. The royal palace met all the expenses for the celebrations of that Ayilyam. Thus, the Ayilyam of Thulam came to secure a royal splendor and henceforth became the festival of masses.

The Ayilyam days of Kanni and Kumbham are still celebrated with befitting grandeur. The Ayilyam in Kanni is the birthday of Nagaraja and that in Kumbham is the birthday of Anantha, the Muthassan of Nilavara (cellar).

All the three Ayilyams – Kumbham, Kanni and Thulam have Ezhunalathu. During Ezhunalathu, Valiya Amma carrying the idol of Nagaraja, leads a spectacular procession from the temple to Illom. She is followed by Cheriya Amma carrying the idol of Sarpayakshi Amma and the two senior-most male members carrying on their head the idols of Nagayakshi Amma and Nagachamundi Amma. Once reaching Illom, she performs her daily Thevaram, followed by Ayilyam pooja. Ayilyam pooja is performed on every Ayilyam but Ezhunalathu takes place only during the months of Kumbham, Kanni and Thulam.

Pulasarppam Pattu is an annual offering in Pulakkavu, situated to the north-east of Illom. The main Pooja here is Nurum Palum. Valiya Amma has the right to offer pooja. (Nurum Palum is offered here regularly on Ayilyam Day in Kumbham or on any other Ayilyam coming thereafter).

Mahasivaratri, the day of the great festival in Siva temples, is given equal importance Mannarasala. The installation of the Nagaraja is in accordance with the concept of Siva. The poojas also are on the Saivite model. Thus, Sivaratri assumed special importance among the annual festivities. The festivities on Sivarathri day at Mannarasala are also associated with Vasuki, the King of Serpents. Legends say that once Vasuki went round the gigantic Thanni tree in front of the temple in a sportive mood and stretched his hoods shining with jewels towards the east; opened his mouth and hissed; all the sands in that place flew away; and a little pond came into being. This is Karoli pond (Karoli Kulam). On Sivarathri day, it is believed, he goes in procession in that direction to have a glimpse of his playful creation.

Only on Sivarathri, Deeparadhana (evening pooja) is performed at Mannarasala. The senior-most male member of the family performs this pooja. On completion of the 'Athazhapuja (evening worship), Valiya Amma begins to perform Sarpabali.

The poojas for Sarpabali are performed by Valiya Amma herself on the platforms in front of Nagaraja and Sarpayakshi. The members of the Illam grind rice in the mortar for the Nurum Palum of the Sarpabali on Sivarathri day. The Sarpabali is the offering made by the Illam. Hence, grinding rice is a voluntary sacred offering by the members in the family. That only on Sivarathri day is the Sarpabali which is pleasing to Nagaraja offered on behalf of the Mannarasala family because of the special attachment to Siva, the Sarpabhushana (one who wear serpents as ornaments). In the last quarter of the night - the images of Nagaraja and Sarpayakshi from the temple are carried on head by the senior most male members are taken out in ceremonial procession towards the due east of the temple and placed at the foot of a divine tree about half a kilometre away. The journey is around the Illam; when the procession returns to the sanctum sanctorum by the southern side of the temple, the scarlet glow of the rising sun will have come up in the sky. The bright light of the traditional torches (theevettis), silver umbrellas, decorative discs and fans (Aalavattam and Venchamaram), all accompanied by musical instruments add to the grandeur of the celebrations. Sarpabali is more of a ritual of the members of the Illam, when compared to other festivities where devotees are offered to take part and share the devotion of the festival.

Only once a year Nurum Palum is offered and performed in the cellar (Nilavara): that is on the day next to Sivaratri. On the fifth day after Sivaratri, the Mother comes to the Illam after the daily pooja in the temple, and opens the cellar. The prasadam of the Nurum Palum is distributed among the members of the family by the Mother. After the pooja in Nilavara, Nurum Palum and other poojas are performed in Appooppan Kavu (Grandfather’s Grove), which is the abode of "Muthassan".

Sarpam Pattu is the most pleasing of all poojas to the serpents. Though a very rare and laborious process in terms of the poojas and execution, this holy ceremony is to be conducted once every forty-one years. Only a few blessed ones gets to witness this pooja twice in their lifetime. There are records of Sarpam Pattu held several times. After 1073 M.E. it had been continuous except for once. The details of the Sarpam Pattu of 1074 have been recorded clearly. Thereafter in 1151 (1976) M.E. this ceremony attracted public attention.

Conducting Sarpam Pattu requires huge spending and manpower for many months. Six to Seven Kanyakas (virgin Brahmin ladies), Cheria Amma and Valiya Amma participate in the poojas that may last for many weeks, until Valiya Amma realises in her trance that Nagaraja is satisfied with the pooja. Separate poojas are offered to the nine Nagas namely Nagaraja, Sarpa Yakshi, Naga Yakshi, Naga Chamundi, Nilavara Muthassan, Kuzhi Nagam, Kari Nagam, Mani Nagam and Para Nagam during these days. The ladies of the family who partake in this festivity avoid rice meals during these days, as part of the rituals.

The Yajnavedi (the altar of sacrifice) is in the yard, south of the cellar. When floor decorations, songs, serpent dance, and sacrifice for serpents as well as Nurum Palum are performed in the presence of Valiya Amma, the place around the altar becomes a fantasy world of devotion, thanks to the songs of poojas and dances, the many types of musical performances, the decorations, the accompaniments etc. At such times the temple gates are not closed. The rituals that go for days and nights last until the day when Valiya Amma becomes divinely possessed and makes prophetic announcements.

The year after the Sarpam Pattu is celebrated Pallippana. It is the 'pana' performed by the Velan tribe. Gandharva song is held during the year after Pallippana. The 'Kurups' draw the figures on the ground known as Kalam, Valiya Amma performs the Pooja; and this is known as Gandharvan Pattu.