Jogen Chowdhury was born in Faridpur (present-day Bangladesh) in 1939. In 1948, the family moved to Calcutta (now Kolkata) after the Partition of India. He graduated from the Government College of Art & Craft, Kolkata in 1960. Later, he joined Beaux-Arts de Paris for further studies. The trauma of being uprooted from the birthplace which he went through during the Partition finds expression in his paintings. His student years in Paris helped him to develop his unique style.

The artist has participated in various solo and group exhibitions in India and foreign countries. He is the recipient of Prix le France de la Jeune Peinture (Paris) in 1966. In 2001, he was awarded the Kalidas Samman by the Government of Madhya Pradesh.