National headquarters are located in Honkomagome, Bunkyō, Tokyo, Japan, supplemented by prefectural branch offices and member associations in local communities.

[1] Those physicians formed the Imperial Medical Association (帝国医会, Teikoku ikai) in 1890 to advocate for the practice of Chinese (kampo) medicine, but the IMA was dissolved in 1898.

[2][3] During World War II, the JMA served as the sole national association responsible to maintain and improve clinical health for the Japanese public.

[3] During the post-war period the Japan Medical Association underwent reforms with direct intervention from the GHQ of the Supreme Commander for the Allied Powers.

The most notable reform involved persons who had contributed to the war effort and who would no longer be permitted to accept executive appointments in the ongoing business of the association.

[4] Without the demands of World War II on the medical fraternity, the association was able to refocus efforts on school, occupation, and community health in addition to standard clinical healthcare.

[11] For a period of almost ten years, from 1947 to 1956, the association defended physicians' rights to prescribe, formulate, and sell medicine, which the government proposed to prevent through a parliamentary bill.

[13] As Kodate notes, while there has not yet been "the emergence of a new accountability regime, increased pressure is now placed on healthcare providers in terms of monitoring performances, collecting information and making decisions on how to act when serious incidents occur.