Rao received most important scientific awards and honours including the Marlow Medal, Shanti Swarup Bhatnagar Prize for Science and Technology, Hughes Medal, India Science Award, Dan David Prize, and Royal Medal. He also received Padma Shri and Padma Vibhushan from Government of India. On 16 November 2013, the Government of India selected him for Bharat Ratna, the highest civilian award in India, making him the third scientist after C.V. Raman and A. P. J. Abdul Kalam to receive the award. He received the award on 4 February 2014 from President Pranab Mukherjee at the Rashtrapati Bhavan.