Dr. Shekhar Agarwal is a recipient of Vishisht Chikitsa Ratan Award from the Government of Delhi, which was bestowed on him, in 2012, for his services to the field of medicine. He has also received some other awards such as:

1. Proxime Accessit Award for the M.Ch.(Orth) Thesis from the University of Liverpool, UK, 1985 on “Renal Transplantation and Locomotor Disease” – Published in Clinical Orthopedics and Related Research from USA.
2. Xavier Gold Medal – 1969; highest award from school for outstanding performance, academic excellence, leadership, and integrity of character and conduct.
3. Matre Shri Award in 2003.
4. Life Time Achievement Award at the Golden Jubilee Celebrations of St.Xaviers School in 2009 for CreativeApproach in his profession and dedication and service to humanity.
5. TOI Health Achievers Award 2017.
6. Life Time Achievement Award in Health Care – 2019 by National Healthcare Leadership Congress & Awards.