Nagarajan's parents are immigrants from India. Her mother, Geetha Nagarajan, is a former developmental specialist at Western Psychiatric Institute & Clinic. Her father, Nandu Nagarajan, is a professor and academic at the Joseph M. Katz Graduate School of Business at the University of Pittsburgh. She has one brother, Arjun.
Anisha Nagarajan was raised in the Squirrel Hill neighborhood of Pittsburgh, Pennsylvania, before moving with her family to the suburb of Fox Chapel.She spent a year at a boarding school in India when she was 15 years old before graduating from Fox Chapel Area High School in 2002. She enrolled at New York University (NYU) after high school. She was cast in the Broadway musical Bombay Dreams as Priya during her sophomore year at NYU. She married her husband, actor Aalok Mehta, who co-starred in the musical.
Nagarajan appeared in a number of regional theater productions following Bombay Dreams, including the Hangar Theater production of Rent in Ithaca, New York and the The Wiz at the La Jolla Playhouse in San Diego, California. She is currently finishing her bachelor's degree at New York University.
In 2010, Nagarajan was cast as Madhuri, a shy call center employee in the NBC series, Outsourced. The role is her largest television credit to date. She had previously appeared in a guest role on the ABC television series, Ugly Betty.