The Academy is currently organization attached to the Ministry of Education, Culture, Sports, Science and Technology; and the organization's headquarters located in Ueno Park, Tokyo, Japan. Election to the Academy is considered the highest distinction a scholar can achieve, and members enjoy life tenure and an annual monetary stipend.

In an effort to replicate the institutional landscape found in many Western nations, the leaders of the Meiji government sought to create a national academy of scholars and scientists modelled to the British Royal Society. In 1879, Nishi Amane was made the head of what was then called the Tokyo Academy.

The Imperial Prize and Japan Academy Prize are awarded to persons who have achieved notable research landmarks or who have authored outstanding academic papers or books. One of the Academy's most important functions involves conferring these prizes, which have been awarded annually since 1911. Since 1949, these prize award ceremonies have been graced by the presence of HIM the Emperor of Japan; and since 1990, both the Emperor and Empress have attended.