Gupta received the Distinguished Teacher Award from the Institute of Kidney Diseases and Research Centre (IKDRC), Ahmedabad in 2000 and the President's Gold Medal of the Urological Society of India in 2003. The Medical Council of India awarded him Dr. B. C. Roy Award, the highest Indian medical award, in 2005, and he received the Fellowship of the UICC ICCRT, the same year. The Government of India awarded him the Padma Shri, the fourth highest civilian honour, in 2007, the same year as he received the Eminent Men for Distinguished Achievement of Highest Order from the Indian Medical Association. He received the Urology Gold Medal from the Urological Society of India and the Ranbaxy Research Award in 2009. Rani Durgavati University honoured him with the degree of Doctor of Science (honoris causa) in 2009 and the Urological Society of India awarded him their Lifetime Achievement Award in 2010.
