Wako University was founded in 1966 as a four-year liberal arts institution of higher learning.

In 2004, Wako University accepted one applicant, however, upon learning that the applicant was the daughter of Shoko Asahara, the mastermind behind the Sarin gas attack on the Tokyo subway, they rescinded her acceptance.

This was a controversial event and an assistant professor, Eiji Otsuka, resigned in protest.

The president of the university at the time, Osamu Mitsuhashi, was a professor of sociology who had recently published the book "Notes of Discrimination".

In end, the university was sentenced by Tokyo District Court to pay a fine of ¥300,000 (US$2,500).