St. John’s College started as an English Training Centrefrom2010 to 2011 with only three students, two (Andrea Ngong Deng and John Bol Angui) of whom failed special entry examinations of Bishop Gwynne College in Juba. Those two students were coached in English Language, by Bishop Moses Deng Bol – Bishop of Wau Diocese and the then Diocesan Secretary Rev. Andrew Apiny, to improve their English Language to enable them to pass the special entry examinations in order to be admitted to Bishop Gwynne College in Juba.
In 2012,Bishop Moses Deng Bol opened a Theological College to train pastors who were ordained, without theological training, during the 21 years of Sudan civil war and appointed Rev. Joseph Mamer Manot as the first Principal of the College in July 2012. Two (Andrea Ngong Deng and Samuel Mabith) of the three students became the first batch of the College in 2013 and one of them went back to St. Paul’s University where he was admitted for a three years Diploma programme in Theology.
In April 2016, Archbishop Daniel Deng Bul graduated the first batch of Theology students from the College, while in the same year, Archbishop Moses Deng Bol thought of adding new two Departments of Primary Education and Business Administration.
Currently, the College is running three departments of Theology, Primary Education and Business Administration & Management. The Department of Theology is the oldest one, while the Department of Business Administration & Management is the largest Department at the College. Annually, College plans to admit 200 students across various fields of specializations.