The award was presented by the Duke of Cambridge for services to Paralympic Sports Medicine and the British Paralympic Association.
Prince William thanked him for his work and commented “and so all these medals are down to you!”
They discussed how Professor Webborn had been injured whilst in service in the Royal Air Force and how he was now helping support the work of Prince Harry in the Invictus Games.
Professor Webborn also met the newly-knighted Sir Rod Stewart and the ceremony was followed by a luncheon with family and friends at the Royal Society of Medicine.
Professor Webborn said: "It was the proudest day of my life. Driving into Buckingham Palace with your family is a bit surreal. The Royal Household staff were all so wonderful and helpful, making a very nervous occasion stress-free. I am so pleased I could share this day with all my children. I know that my parents would be looking down with great pride too."