Sloane returned to London to practice medicine. Thomas Sydenham, a physician noted for his application of scientific observation to medical cases, became an advocate for his career and introduced him to prospective patients. On April 13, 1687, Sloane was admitted as a fellow to the Royal College of Physicians, London.
In the same year, Sloane became the personal physician to Christopher Monck, the second duke of Albermarle. The Duke was leaving to become Governor of Jamaica and Sloane was eager for the opportunity to study new plants and drugs. Sloane was in Jamaica from December 1687 to March 1689. The Duke had died in October 1688, but his household was unable to return to England immediately because of the ongoing revolution. During his stay in Jamaica, Sloane kept notes about the weather, the landscape and the plants. He also collected samples, including 800 plants, many of which were new to Europe. Sloane remained in the employ of the Duchess of Albemarle for nearly four years before setting up his own practice in Bloomsbury, a fashionable part of London.