Prabhakaran was born in Kodungalloor in the Thrissur District of Kerala. He is the fifth and youngest son.

His father, who was working in the Army, passed away when Prabhakaran was in his teenage years. When he turned 18, taking his mother's suggestion, he moved to Chennai, enticed by the possibilities in the Madras Regimental of the Indian Army. But he was rejected. 

He stayed there for several months with his father's friends and searched for all kinds of jobs. Since nothing worked out as expected, his mother suggested that he go to her brother, who was Prabhakaran's uncle.

His uncle had been in Ceylon (Sri Lanka) a few years back. When the economy of that country plummeted, he embarked on a small ship to India. However, he accidentally landed at Vishakapatnam harbour, even though his original plan was to reach Chennai. When he landed in Andhra Pradesh, he changed the actual plan he had and moved to Machkund, a small village in Odisha which shares a border with Andhra.

"Nothing was there at that time, not even a shop," Prabhakaran said. 

He set up a small tea shop. One of the reasons for choosing this place was a dam which was under construction at that time.

Years later, his mother asked Prabhakaran to go to this place, Machkund. He went and learned the skills to become a hotel proprietor. Years later, Prabhakaran married an Odia girl and now has a daughter and son. The daughter is married there with a 9-year-old son. Prabhakaran is 76 now. He had a stroke a few years back, but is still able to manage walking.

Prabhakaran shared: 

In those days, when he had reached here, it was relatively easy to get a job at the Machkond dam site, under the Electricity Board of Odisha. All he had to do was fill out a form and have it signed by a witness. Prabhakaran filled out the form and gave it to his mother-in-law to sign.

At that time, the salary scale was low, actually less than half of what Prabhakaran earned from the hotel. So, without considering Prabhakaran's wishes, she tore up the form. Later, the salary scale changed many times.