After Waddell worked as a Professor of Chemistry and Pathology for 6 years, he became involved in military expeditions across Burma and Tibet. Between 1885–1887 Waddell took part in the British expedition that annexed Upper Burma, which defeated Thibaw Min the last king of the Konbaung dynasty. After his return from Burma Waddell was stationed in Darjeeling district, India, and was appointed Principal Medical Officer in 1888. In the 1890s Waddell, while in Patna, established that Agam Kuan was part of Ashoka's Hell. His first publications were essays and articles on medicine and zoology, most notably "The Birds of Sikkim" (1893). In 1895 he obtained a doctorate in law.