"The Guruvayoor temple is divine and magnificent. Prayed at this iconic temple for the progress and prosperity of India," Modi tweeted.
He also posted images of his visit to the over 5,000-year-old shrine on the micro-blogging site.
After the prayers, Modi held a meeting with the officials of the temple along with Kerala Governor P. Sathasivam, Union Minister of State for External Affairs V. Muraleedharan and State Devasom Minister Kadakampally Surendran.
Temple authorities presented him a memorandum to the tune of Rs 450 crore for various developmental projects of the shrine.
Upon his arrival, the Prime Minister was given a traditional welcome by priests.
The entire top brass of the Kerala unit of the Bharatiya Janata Party (BJP), including Rajya Sabha member and superstar Suresh Gopi, who unsuccessfully contested the Thrissur Lok Sabha seat in last month's general elections, were present at the temple town.
Modi flew into Guruvayoor from Kochi earlier in the morning.
He participated in various rituals in the temple, including reading of the 'Vishnu Sahasaranamam'.
Modi had visited the temple in 2008 soon after he became the Chief Minister of Gujarat for a second time.
Before returning to the national capital later in the day, Modi will address a public rally near here.
( With inputs from IANS )