Urology as a medical science was first brought in Japan from Germany in the early years of Meiji era, together with Dermatology. Therefore, "Dermatology and Urology" was the name of the Department in Medical Institutes in Japan.

From these reasons, JUA had close relationship with Japanese Dermatological Association. The origin of Japanese Dermatological Association (JDA) was the Society of Dermatological Disease which was established in December, Meiji 33 (1900). The first annual Meeting of JDA including urological section was held in April, Meiji 34 (1901) and the first Journal of Dermatology and Urology was published in March, Meiji 34 (1901).

Urological Associations became independent one after another In Europa and America,, and the first Meeting of the International Society of Urology was held at Paris in Meiji 41 (1908) .

The first meeting was held to inaugurate the Association of Urology in January, Meiji 45 (1912) among the leading Urologists who learned Urology abroad followed by the first annual Meeting of Urology under the name of Society of Urological Diseases in April, Meiji 45 (1912). JUA was established in April, Showa 3 (1928), and the Japanese Journal of Urology was published in the same year which was the17th issue of the Japanese Journal of Urological Diseases. The annual Meeting of JUA was held together with JDA between April, Showa 4 (1929) and April, Showa 30 (1955). The annual Meeting of JUA became completely independent form JDA since the 44th annual Meeting of JUA in April, Showa 31 (1956).

The system of a urological specialist was enforced in Showa 61 (1986), and JUA became a corporation in August, Heisei 3 (1991). In Heisei 6 (1994) the International Journal of Urology was issued as an English version of the formal Journal of JUA in addition to the Japanese Journal of JUA.
The president of JUA is in the present time Professor Akihiko Okuyama, M.D. since April, 2005, and the total number of members of JUA is 7,636 (April 2008).