Gakushuin's origins lie in the "Old Gakushuin" established in 1847 in Kyoto as the educational institution of the Imperial Court. As things began to change during the final period of the Tokugawa Shogunate, the Emperor Ninko began the process of establishing a place of study and learning with the intention of raising the educational level of the Imperial Court and improving its manners and morals. Emperor Ninko passed away before the project was completed and it was ultimately inaugurated, in line with his dying wish, by the newly succeeded Emperor Komei. The origin of the name "Gakushuin" is said to have come from the Japanese reading of the Chinese characters for "to be taught" and "to learn" in the following quotation from the Analects of Confucius: "To be taught and to learn the truth is such a precious thing."

In 1877 a new set of school buildings, which had been constructed on a campus at Kanda Nishikicho bestowed by the Imperial Household, was inaugurated at a ceremony held in the presence of the Emperor and Empress. In order to follow in the footsteps of the Kyoto Gakushuin, the Emperor Meiji gave the name"Gakushuin" to the new school as well.

In 1884, having started out as a private school for the nobility, Gakushuin became a government school under the jurisdiction of the Imperial Household Department, with entry now open to children from outside the ranks of the nobility as well. Then, following the establishment of a higher education section, lectures in subjects such as politics, law and literature were held for 12 years between 1893 and 1905.

After a transfer to Toranomon, a new school was built at Yotsuya in 1890. The move to the present site, at Mejiro, took place in 1908. That site measured a vast 200,000 square metres.

In 1947, after the Asia-Pacific War, the ordinances of the Imperial Household and of the Department of the Imperial Household relating to Gakushuin and to the Gakushuin Girls' School were abolished, thus announcing the end of both Gakushuins as government schools. At the same time, all limits on entry were removed and Gakushuin became a purely private school, to which anybody could gain entry if they were able to pass the entrance examination.

In 1949 --- the year when, as a result of educational reforms, the Japanese university system was modified --- Gakushuin established a university. It started with a Faculty of Letters and Politics, comprising a Department of Philosophy, a Department of Letters and a Department of Politics, and a Faculty of Science, which had a Physics Department and a Chemistry Department. This developed into the present day university, with its 14 departments in four separate faculties. In addition, with a fully equipped Graduate School comprising six separate schools and 14 specialist courses, Gakushuin offers students ample opportunity to build on the basis of their undergraduate education, in terms of both breadth and depth, by pursuing further academic research.

With a total student body of around 9,000 and a large and distinguished teaching staff from the very forefront of the academic world, Gakushuin offers, as well as normal lectures, one-to-one guidance through seminars, the preparation of graduation theses, scientific experiments, special research, etc.