In addition to writing numerous works of fiction and non-fiction, Mukherjee taught at McGill University, Skidmore College, Queens College, and City University of New York before joining Berkeley.
- The Tiger's Daughter (1971)
- Wife (1975)
- Jasmine (1989)
- The Holder of the World (1993)
- Leave It to Me (1997)
- Desirable Daughters (2002)
- The Tree Bride (2004)
Short story collections
- Darkness (1985)
- The Middleman and Other Stories (1988)
- A Father
Memoir
- Days and Nights in Calcutta (1977, with Clark Blaise)
Non-fiction
- The Sorrow and the Terror: The Haunting Legacy of the Air India Tragedy (1987, with Clark Blaise)
- Political Culture and Leadership in India (1991)
- Regionalism in Indian Perspective (1992)