Vallikunnu got its name after the river "Valliyar", which flowed encompassing the hilly area. This gramam got place in many old literatures of Kerala. Ullur S Parameswara Iyer mentioned in his great work "Kerala Sahithya Charithram", that the "Valli Gramam" referred in "Basha Naishadam Chambu" of Mazhmangalam is Vallikunnu Desam. This Desam was under the administration of the Royal Family of Parappanad. The Monarchy of Parappanad kingdom led to the development of this village. The Head Quarters of Parappanad Kovilakam was in Neduva village of Parappanangadi panchayath. We can see Remains of Parappanad palace, Oottupura, and Kolappura in Neduva village. For administration purpose this place had been divided into five "Tharakoottangal" by the rulers. This tharakoottangal was centered on Siva temples. These Tharakoottams are: 1. Vallikunnu(Thekkil SivaTemple) 2. Mannur( Mannur Siva Temple) 3. Chelembra (Elannummal Siva Temple) 4. Thenhipalam(Pappannur Siva Temple) 5. Vennayoor(Vennayoor Siva Temple)

The armory and training centre of Parappanadu Kingdom was situated in the place where Mekkotta Bhagavathy Temple now exists. The remains like tunnels and trenches seen around Mekkotta Temple are evidences for this. According to some historians, ancestors of Velu Thampi Dalava belong to Vallikunnu, and later they migrated to Tiruvithamkur. The old port named 'Thindis 'belongs to vallikunnu. Now the place is known as Kadalundi Nagaram. It is to be believed that the birth place of A.R. Raja Raja Varma, the famous Malayalam Pandit was in vallikunnu.

Vallikunnu contributed many freedom fighters to Indian freedom movement. Sri K. Madavanar, Sri Puliyasseri Sankunni Nair, Sri Idasseri Purushothaman Namboothiri, Sri K. T. Madhavan Nair, Sri C. M. Echunni Nair, Sri Paanat Kunhiraman Nair, Sri U. Kandan Kutty, Sri K. Ayyappan Nair. Sri P. Kunhiraman Master was some of them. Vallikunnu Panchayath came into existence in 1962. The first President of Vallikunnu Panchayath was Sri Vadakkunthanni Kunhiraman Nair. Sri P. Kunhiraman Master, Sri Koothirezhi Ayyappan Nair, Sri U. Theyyam Vaidyar, Sri K. V. Govindan Kutty Nair, Sri K. T. Madhavan Nair was the former activists in educational sector.