The existence of temple was first mentioned in Sangam Literature as one of the major temples under Chera Dynasty. Cheras were adherent worshipers of Lord Shiva. When Chera dynasty ended, the place fell into the hands a few Nair nobles who renamed the place as Ernakulam (corrupt form of original word- Eere Naal Kulam meaning Pond with water always) in recognition of the famous sacred pond of this temple.
Soon this area came under reign of Kochi Kingdom. The Kochi Rulers, due to the siege of Fort Kochi by the Dutch in the 17th century, moved their capital to Ernakulam and established a Palace close to this temple, facing the temple pond (The Tank Shed Palace seen behind current Durbar Hall). This helped the temple to gain prominence, due to royal patronage. The temple deity was declared as protector of Ernakulam city (Nagara Devata),
The second phase of the temple came in 1842 when Diwan of Kochi, Sri Edakkunni Sankara Warrier felt to renovate the temple which were in dilapidated condition. Works were started in 1843. Two new Gopura Mandapams (Entrance Towers) were constructed in traditional Kerala style similar to Sree Poornathrayesa Temple of Tripunithura which was the Chief Royal temple of Kochi Maharajas. The new temple complex was opened to public in 1846. The temple was elevated to a royal temple and brought under direct administration of Kochi Government's Devaswom Board. In 1949, when Kochi acceded into India Union, the Devaswom Board came under new Government's control, which still remains.
As part of increasing local participation in temple management, the Ernakulam Kshetra Kshema Samithi consisting leading Hindu members of Ernakulam city did participate in the fund collection to purchase the land adjacent to the temple. They purchased the property which was in the possession of Corporation of Kochi. The activities of Ernakulam Kshethra Kshema Samithy did good to the overall development of the temple.
Adjacent to the main Shiva Temple, two other temples are constructed in the temple grounds, which makes the Ernakulam Temple Complex. On the Northern side, a Murugan Kovil built in Tamil style can be seen. It was constructed by Tamil residents of Kochi during the administration of Diwan Venkataswamy who was a Tamil Brahmin.
The Muruga Kovil is managed by Tamil Brahmin Association of Ernakulam and all rituals in this temple are in accordance to Tamil style. The presiding deity is Lord Muruga with his consorts Valli and Devanyani. There are two separate shrines forNavagrahas and Ganesha, apart from regular poojas for Vishnu, Dakshinamoorthy and Durga Devi.
The Hanuman temple is built in Udupi Madhwa Sampradaya style
On the eastern side, a Hanuman temple built in Kannadiga Udupi style can be seen. It was constructed by Diwan Venkat Rao in year 1850 as part for his dream to have a temple in traditional Udupi Madhwa Sampradaya style. This is one of the very few temples constructed in Madhwa Sampradaya without Krishna as main deity.
The presiding deity is Lord Hanuman facing towards Shiva temple on western side. A small idol of Lord Rama also worshiped in main sanctum sanctorum. Apart from this, shrines for lord Nagaraja and Raghavendra Swami are also worshipped.
Apart from the temples, the famous Ernakulam Temple pond is located in eastern side, facing opposite to Murugan temple. There is also offices of Ernakulam Brahmin Association and its marriage hall apart from offices of Temple advisory committee.. A 200-year-old banyan tree can be seen near to Hanuman temple.