She was named one of Forbes 30 under 30,[1] MIT Technology Review's 35 innovators under 35,[2] a World Economic Forum Young Global Leader,[3] and a winner of the Carnegie Science Award.

[5] Kundu's research focuses on "transport-based morphometry," or TBM, which applies machine learning techniques to identify latent disease not readily observable by humans reviewing traditional magnetic resonance imaging (MRIs).

[9][10] Kundu has authored or co-authored eighteen peer-reviewed articles, including in the journals Nature Medicine[11] and Proceedings of the National Academy of Sciences[12] and has presented at the International Conference on Acoustics, Speech, and Signal Processing.

She was also named one of MIT Technology Review's 35 innovators under 35 for her creation of "an artificial-intelligence system that can analyze them [medical images] to find patterns undetectable to the naked eye.

[18][19] In 2017, an Elle magazine article remarked, “Not only is she one of the world’s youngest MD-PhD scientists, she has developed technology that could possibly diagnose diseases as early as three years before the symptoms manifest in the patient and she actively works towards the inclusion of more women in STEM (Science Technology Engineering and Math).”[8] In 2016, Dr. Kundu was recognized in Pittsburgh Magazine's "40 Under 40," which wrote "The lightning speed of Shinjini Kundu’s academic progress could test the laws of physics, much less those of probability.