Jogen was born in Daharpara Village, a village in the Faridpur district of Bangladesh in 1939. His father Pramatha Nath Chowdhury was a Brahmin zamindar. Jogen received the interest on art from his parents as both his parents were artists. Pramatha Nath was interested in Hindu mythological incidents and characters. He had painted several mythological scenes from the village theatres. He had also sculpted various Hindu deities. Jogen mother was an expert in Alpana drawings. Jogen Chowdhury was born and brought-up in a village culture and atmosphere. Just before partition Jogen along with his father came to Calcutta; the rest of the family moved to Calcutta in 1948, after the partition. The family stayed at his uncles quarter. Here Jogen painted his first painting, on the wall. In 1951, Jogens family moved to Saheednagar Colony, Dhakuria. Jogen joined the Government College of Art & Craft, Kolkata in 1955 where from he graduated by 1960. His first job was as an art teacher in Howrah Zilla School. After two years in 1962, he was employed as Designer in the Handloom Board, kolkata.