Shaji N. Karun was born on New Year's Day, 1952 as the eldest son of Mr. N. Karunakaran and Mrs. Chandramati in present day Kollam district in the former state of Travancore state, India. The family moved to Thiruvananthapuram, the capital of the state in 1963. He did his schooling in Palkulangara H.S. and took a Bachelor's degree from University College, Thiruvananthapuram. In 1971 he entered the Film and Television Institute of India where he took his diploma in Cinematography. After a brief stint in the south Indian city of Madras, he returned to Thiruvananthapuram in 1976 where he got an appointment as film officer in the newly formed state Film Development Corporation. His association with the legendary Malayalam film maker G. Aravindan began at this time. Then he continued working with notable directors like G. Aravindan, K. G. George and M. T. Vasudevan Nair as a cinematographer.