Aoki began his studies under the Choshu domain doctor Nomi Toan (1794-1872), who taught him traditional Chinese medicine. At the age of 30, Aoki moved to Edo to study Dutch medicine and language in Fukugawa under the physician Tsuboi Shinodo. Thereafter, he continued his studies in Nagasaki, and, in 1851, he was appointed doctor to Mori Takechika, lord of Chosu domain. His brother Kenzo was also a noted physician, and together the two men led a vaccination program against smallpox and cholera in Choshu.
In 1859, Shusuke rebuilt the family home in Hagi to receive medical students from all over Japan. Today, the house has been preserved as part of Hagi's historical heritage and displays memorabilia of the Aoki family, including some silver coins discovered in a warehouse and inscribed with "Ao Ken," for Aoki Kenzo. There is also a display of the life of Kenzo's adopted son, Aoki Shuzo. Known as Viscount Aoki affter the creation of the peerage system in the Meiji era, Shuzo was Japan's third foreign minister and Japan's ambassador to the United States from 1906 to 1908.