Jogen Chowdhury was born in a village near Kotaliparha at Faridpur district at what is now Bangladesh in 1939. The family moved to Calcutta in 1947 following the Partition of Bengal.
Chowdhury entered the Government College of Art and Crafts in 1955 and graduated from the college in 1960. Chowdhury's first job was as an art teacher in a school in Howrah. He taught there for two years and then in 1962, he joined a textile designer in the Handloom Board In 1965, Chowdhury went to Paris and studied in Ecole des Beaux Arts and in William Hayter's Atelier 17. He returned to India in early 1968 and went to Madras as a textile designer in the Handloom Board. He stayed there for four years till 1972.