Chakrabarty is a fellow of the American Physical Society and a legacy fellow of the American Astronomical Society. His other awards include the 2006 AAS Bruno Rossi Prize in High Energy Astrophysics, an Alfred P. Sloan Research Fellowship, the MIT Buechner Teaching Prize in Physics, and the inaugural 2017 MITx Prize for Teaching and Learning in MOOCs for his work on the 8.01x Mechanics Series. He recently chaired the Panel on Compact Objects and Energetic Phenomena of the Astro 2020 Decadal Survey on Astronomy and Astrophysics, sponsored by the National Academy of Sciences.