The institution was founded in 1978 as Pacific & Asia Christian University (PACU) by Howard Malmstadt and Loren Cunningham, the founder of Youth with a Mission, in Kailua-Kona, Hawaii.

[citation needed] Australia's higher education and training system lists University of the Nations' affiliated Institute for the Nations and Youth With A Mission programs in five locations as registered training organisations authorized to provide certificates and diplomas in several specified fields.

[7] In January 2018, Pablo Rivera, the chief financial officer for University of the Nations in Kona, pled guilty to wire fraud.

[15] Before the fraud was exposed, the school's financial situation was critical, increased charges were applied to volunteers and students.

[16] In October 2020, University of the Nations in Kona was associated with the largest single day increase of COVID-19 outbreak on the Island of Hawaiʻi up to that date.