Upon his return to Britain, Ninnis qualified in January 1867 for the title of Surgeon in the Royal Navy by passing examinations at the Royal College of Surgeons; the following month he was appointed to the Royal Naval Hospital in Greenwich, where he remained until 1869. On 21 December 1874 he was promoted to Staff-Surgeon Second Class. In May 1875 he was appointed to HMS "Discovery", one of two ships—the other HMS "Alert"—which comprised the British Arctic Expedition, led by Captain Sir George Nares. The expedition aimed to be the first to reach the North Pole, pushing north through Smith Sound, between Ellesmere Island and Greenland. The two ships made slow progress up the sound, repeatedly halted by dense pack ice. During August of the first year, the expedition's Greenland Dogs began to show signs of disease; the dogs experienced fits and "madness", owing, it was assumed, "to close confinement, wet decks, and want of natural exercise." Ninnis and Fleet-Surgeon Thomas Colon of the "Alert" were charged with investigating the disease. Ninnis' report to Nares noted the disease's similarity to rabies, "but there is no instance recorded in Greenland of human beings who have been bitten having suffered from hydrophobia symptom of advanced rabies, and the recovery of the animals in some instances is entirely opposed to the recorded experience of true rabies."