Japan Christian Junior College grew to have a student enrollment of nearly 600 by the mid-1990s, with a faculty of nearly 40 part-time and full-time teachers and professors.
However, within a decade, student enrollment had dropped significantly, forcing college administration to make drastic changes.
In 2006, Japan Christian Junior College received full accreditation and Government Recognition from the Ministry of Education for its two areas of study — English and Christianity — with all diplomas and degrees retroactively regarded as equivalents to an American Associate's of Arts degree.
After an announcement by the Board of Regents, with the support of the General Church of the Nazarene, in the spring of 2006, Japan Christian Junior College closed and ceased operations on March 31, 2009.
Reasons cited concerned a lack of students (attributed to the falling birth rate in Japan), loss of revenue, and departure of American teachers.