Poonthanam was born in 1547 in the month of masi on the day of Aswini, at Keezhattoor, near Perinthalamanna in Malapuram district,into a Namboodiri Brahmin family. He married at 20, but for a long time, they had no children. He began to propitiate the Lord of Guruvayur by reciting the 'Santhana Gopalam' and a son was born. He called for a celebration and everybody known was invited, but the child died an hour before the Annaprasanam ceremony. Grief-stricken, Poonthanam sought refuge at Guruvayur and started praying with the puranic story of Kumaraharanam. The heartbroken Poonthanam, it is said, was consoled by Guruvayurappan himself, who lay down on his lap, for a moment, as a child. He considered Lord Krishna as his son and achieved enlightenement. In the Jnanappana he writes: "While little Krishna is dancing in our hearts, do we need little ones of our own?". Poonthanam spent the rest of his life reading the Bhagavatham and singing the Lord's glories in simple Malayalam. His magnum opus, the Jnanappana, was composed during this period. His house, the Poonthanam Illam is now under the Guruvayur Devaswom.