Lord Guruvayurappan was originally worshipped by Brahma, the Creator. He presented the image to sage Kashyapa, who in turn gave the idol to Vasudeva and Devakai at Mathura in the Dwaapara Yuga. Krishna Himself worshipped the idol at Mathura and later at Dwaraka till the end of His incarnation.. At the time of his departure to Vaikuntam (Heaven), Krishna entrusted the idol to His trusted friend Udhdhava. This friend of Krishna, who had the vision that Dwaraka would be submerged in the sea very soon, took the help of Vayu, the Wind God, and Guru, the preceptor of the Devas, and got the idol installed at a suitable place for the benefit of Mankind. This spot had a beautiful lake of lotus nearby. Lord Shiva and Devi Parvati, who had their abode here, blessed the consecration. The Celestial Architect Vishwakarma is believed to have built the Krishna shrine. Since Guru and Vayu were involved in the installation of Krishna's image, the place acquired the name Guruvayurpura and later became Guruvayur. The lotus lake is the present temple tank Rudra Theertha. Shiva and Parvati later left for Mammiyur on the other bank of the lake. This Shiva shrine is situated close to the Krishna temple.
According to another legend, people suffering from rheumatism once appealed to sage Parasurama, who was around the present Thrissur, for relief. Maharishi Narada, who was traversing through this region, advised Parasurama to bring the image of Sri Krishna from Dwaraka and install it at this sacred spot to enable the people to worship Him. Such is the faith in Sri Guruvayurappan that even today people suffering from rheumatism and such other diseases regularly visit this holy place and get relief.