Rao, who was the first recipient of the India Science Award, won several international prizes and is a member of the world's leading scientific associations, including the U.S. National Academy of Sciences, American Academy of Arts and Sciences, Fellow of the Royal Society, London, French Academy, Japanese Academy and Serbian Academy of Sciences and Arts.
The British Royal Society awarded Rao the Hughes Medal in 2000.
Rao was awarded the Dan David Prize in 2005 by the Dan David Foundation, Tel Aviv University, which he shared with George Whitesides and Robert Langer.