The history of the idol is said to be as follows. At the beginning of the first Kalpam named Brahmakalpam, Mahavishnu gave Brahma an idol and the first book of Bhagavatham. Brahma, later gave this idol to the Prajapathi Suthapassu and his wife Prishni and Lord Maha Vishnu took incarnation as their son. This couple in their next birth were known as Kashyapa and Aditi. They got possession of this idol in that birth also, and Lord Maha Vishnu was again born as their child, the Vamana. The next birth of this couple was as Vasudeva-Devaki and the story repeats. This time the incarnation of Lord Maha Vishu was as Lord Krishna, the most complete man. Lord Krishna, when he built the city of Dwaraka, built a temple for this idol. Before his death, Lord Krishna entrusted Udhava with this idol and asked him to meet Brihaspathy, the Guru of gods.

The Guru along with his desciple Vayudeva (god of air), found a place which was recommended by Lord Paramashiva. Thus the Guru and Vayu installed this deity and Paramashiva named the place as Guruvayoor. And the deity is now known as Guruvayoorappan. The idol is carved out a stone called 'Pathala Anjana Sila' and is utmost sacred. The place selected for the installation was suitably sacred by the presence of Lord Shiva. The place was already sacred owing to the presence of Lord Paramashiva. He was worshiping Lord Maha Vishnu under the waters of the 'Rudratheertham' (the sacred pond near the temple). Later, Lord Shiva emerged out of the waters when the Prachethas, son of King Pracheenabarhis came in search of a place to worship Lord Maha Vishnu. He then revealed the hymn 'Rudra Geetha' to Prachethas And then the Prachethas worshiped Lord Maha Vishnu for another ten thousand years staying in the 'Rudratheertham' After the installation of the idol of Mahavishnu by Guru and Vayu, Lord Shiva moved to the nearby Mammiyoor temple.

According to the stories, Shri Aadi Shankara who is believed to have extra ordinary powers was once travelling by air from Kalady to Shringeri. Even he, who never believed in the worshiping of idols, was forced to come down while crossing Guruvayoor. To appease Guruvayoorappan he worshiped the deity by eight 'Shloka' (four lines of poetry). This is now known as the 'Govindashtakam'. He then spent 41 days worshiping Guruvayoorappan. The daily rituals of worship during the Mandalam period were conceived by Shri AdiSankara at that time.

Near past history is as follows. The temple was renovated by a Pandya king somewhere around 500 years ago. In 1970, in a fire accident, almost all the temple except the Shreekovil was destroyed and the temple was reinstated in its shape in 1971. The temple is not very big compared to some other well known temples. The Gopuram on the eastern side is 33 feet and that on the western side is 27 feet tall.

Guruvayur  (also written as Guruvayoor) houses the famous Sree Krishna Temple. It is called as the Bhooloka Vaikuntam or Dwarka of the South .The Sree Krishna Temple is the fourth biggest temple in India in terms of the number of devotees per day