Johnson was appointed surgeon's mate in the navy, and sailed to Newfoundland and Nova Scotia, visiting the naval hospitals whenever his ship was in harbour. In January 1800 he passed his second examination, and in February he was made full surgeon and was appointed to the sloop-of-war . He accompanied the expedition against the French forces in Egypt, but was forced to return to London invalided. He spent the winter in studying anatomy at the theatre in Great Windmill Street School of Anatomy, and in June 1801 obtained an appointment on the sloop-of-war , and served in the North Sea.