Dr. Deshpande's career started at the Kidwai Memorial Institute of Oncology in 1982. Three years later, in 1985, he returned to his alma mater, Tata Memorial Hospital, and worked there till 2002, as the Chief of Thoracic Services. His current position is as the Head of Surgical Oncology at the S. L. Raheja Hospital, which was taken over by the Fortis Healthcare in 2009, and presently known as Asian Institute of Oncology where he is the executive vice charman. He has also been a consultant oncologist at Lilavati Hospital, Mumbai.