There are many stories that describe the origin of the word Thripunithura. Some latter day Sanskrit enthusiasts ascribe the origin of the name to "Poorna Veda Puri" - the town of Vedas in its entirety. Another possible origin to name comes from the meaning "the land on the shores of Poorna river".

Other stories play on the pun of "Pooni" or "Pooneeram" which means quiver. One of them relates that Arjuna - one of Pandavas - who once visited Lord Vishnu was given an idol and Arjuna carried it in his "pooni" (quiver). While searching for a place to install it, he met Lord Ganapati and sought help. Ganapati found this place and the idol was installed. Another story of the same variety is as follows. At the end of Dwaparayuga, the period of Lord Krishna, the Lord himself presented an idol to Arjuna, one of the Pandavas, and asked him to install it in a proper place. He kept the idol in a bag used to keep arrows, which was called Pooneeram in local language. When he reached the place, he shouted Pooneeram Thura means 'open the bag' in local language. Thus the name Poonithura has come, according to this story.

But all these stories do not take into account the actual meaning of "thura". "Thura" means port where the backwaters open to the sea. This is the portion of the land and water body which is suitable for the launching and parking of boats. The word: "Thuramukham" which means the face of such opening to the sea is used in Malayalam to denote 'port' or 'harbour'. The original Tamil or Dravidian word is "Thurai". Poonithura is just another port or "thura" in the west coast like Poonthura, Vettuthura, Perumathura, etc. The significance of the word 'Pooni' is yet to be established. The waterbodies in the area point to the presence of a thura in the location, before Kochi Azhi was created by a devastating flood. The word "Thura" in Greek means a door or an opportunity, and could also be a loan word introduced by early traders along the west coast.

When the Kings of erstwhile cochin Dynasty made this place their capital, the area where the palaces and the fort are constructed came to known as Thiru Poonithura as the word "Thiru" shows respect. In due course it became Tripunithura.