The school was founded in 1990. Before Keio Academy opened, many children of Japanese nationals on work assignments in the United States returned to Japan to get a high school education. Keio Academy opened so they could get a Japanese education in the United States. As of 1988 the Japanese government had no plans to fund the school. When the school opened in 1990, the university fully funded the school.
In 1994 the school serves grades 9-12. It had 420 students that year, making it the one of the largest Japanese curriculum schools located in the United States. In 1994 Yasumitsui Nihei, the principal, stated that of the 115 recent graduates, many began attending Keio University while only four went to American colleges.
In 1994 the school was accredited by the Ministry of Education of Japan and by the State of New York. That year, Nihei stated that the curriculum at the school would prepare a student for attending an American university.
The school is located about 30 miles (48 km) north of Manhattan. The school has a 27-acre (11 ha) campus. The main school building, called the "Classroom Building," houses classrooms, administrative offices, the counseling room, the Japanese culture room, and the library. The culture room, where traditional Japanese activities are held, is on the first floor, and the library is located on the third floor. Matsushita Hall serves as the cafeteria. The school also has two dormitory facilities. The South Dorm houses the training room, the school's athletic center. The school also has the Health Center, which serves as a clinic.
As of 1994, 60-70% of Keio students board and live in dormitories.
As of 1994, the school does not admit children resident in Japan. That year, Nihei stated that children resident in Japan may attend Japanese school campuses affiliated with Keio University. As of 1994 there was a registration fee of $2,500 ($3977.89 with inflation) and a yearly tuition of $13,260 ($21098.7 with inflation).
The Ministry of Education, Culture, Sports, Science and Technology (MEXT) classifies Keio Academy of New York, Nishiyamato Academy, and Seigakuin Atlanta, in addition to the former Tennessee Meiji Gakuin, as shiritsu zaigai kyōiku shisetsu (overseas branches of Japanese private schools). The Greenwich, New Jersey, Chicago, and Guam schools are classified by MEXT as nihonjin gakkō (Japanese international schools) as they are operated by Japanese associations. Italicized schools, including the Lyceum Kennedy, Sundai Michigan, and International Bilingual School (as of 2000), are/were not recognized as Japanese schools by MEXT.