Their childhood revolved around the importance of education,[6] and he attended the Calcutta Boys' School (CBS).

He moved to the United States, where he studied with Masatoshi Nei,[6] receiving his PhD in human genetics from the University of Texas Health Science Center at Houston in 1979.

In 1994 he joined the faculty of Case Western Reserve University as the James H. Jewell Professor of Genetics.

[9] Chakravarti became director of the Center For Human Genetics & Genomics at New York University on 2 April 2, 2018.

HSCR is now considered a model for the study of complex disease, in part due to Chakravarti's development of experimental techniques.