Ninnis graduated from the University of St Andrews as a Doctor of Medicine on 2 January 1861, and became a Member of the Royal College of Surgeons—MCRS; a professional qualification—in April of the same year. On 1 August, he entered the Royal Navy Medical Service, as an Assistant Surgeon, and was appointed to HMS "Pantaloon". In October 1862 Ninnis was transferred to the navy's flagship HMS "Victory", then moored in Portsmouth. He was posted aboard HMS "Curacoa", assigned to the Australian Station, in 1863.