As per the mythology it is referred in Mahabaratha as the place where Arjuna build this temple for lord Krishna in the Chapter of Santhana Gopala.

The belief is that in Mahabaratha Arjuna dropped his "puni" before lord krishna as a sign of accepting defeat in the great kurukshetra battle.

Later the King of the Princely state of Kochi has shifted his capital to this area from Trichur.

He built palaces and fort on the land which is located on the eastern banks of Poorna River.

Since then this area started to be known as Thiru Poonithura, 'Thiru' being the word in local Malayalam language to express respect.