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The International Reformed Evangelical Seminary (formerly the Reformed Institute) started as a movement led by the Holy Spirit when Rev. Dr. Stephen Tong was on a flight from America to Singapore in 1995. Dr. Tong spoke to two fellow servants of God who similarly felt the movement. After that the Reformed Institute for Christianity and 21st Century began for the first time in Washington DC. In 1996, the intensive lectures for the M.C.S. (Master of Christian Studies) started in Washington DC. This lecture was attended by 108 students from various countries, most of whom held Ph.D. in other fields.

At the same time, the Developing Christian Insight Program (SBWK) also started in Jakarta. These seminars were attended by many people from various professions, ministry experiences, and church denominations. The seminar themes were related to Christian insight in cultural mandates, including: integrity of life, culture, philosophy, epistemology, art, etc. So, when Dr. Tong returned to Jakarta, he inaugurated the M.C.S. Study Program of the International Reformed Evangelical Seminary on Sunday 21 July 1996, during the Sunday Service of the main church (GRII was at Granada Building at that time), with around 120 part-time students and 26 full-time students as the first batch of the B.Th, M.Div and M.C.S Programs. Furthermore, the undergraduate program for Church Music and the Master of Arts program in Evangelism also started.

The lectures were held on Monday to Friday (evening classes) and Saturday (16.00 – 21.00) at Jl. Tanah Abang III/1 Central Jakarta. After running for 2 years, a new milestone was reached in 1998 with the purchase of 12 shophouses at Ruko Prima Sunter, North Jakarta. The courses for full-time students began at Ruko Pinangsia – Lippo Karawaci. After the renovation of the two shophouses of International Reformed Evangelical Seminary, the lectures, library and student dormitories were moved to the two shophouses. In June 2001, with the completion of the renovation of 10 shophouses, all lectures, libraries, lecturers' residences and student dormitories were moved. In July 2011, International Reformed Evangelical Seminary moved its location and now operates within the Reformed Millennium Center Indonesia (RMCI) complex in Kemayoran where the Indonesian Reformed Evangelical Church (GRII) is located. This complex also has facilities such as the Aula Simfonia Jakarta Concert Hall and the Sophilia Fine Art Center Museum.

In line with the efforts to develop its self-potential, International Reformed Evangelical Seminary signed a Memorandum of Understanding (MOU) with Westminster Theological Seminary (WTS), Philadelphia, USA in April 2011, Theologische Universiteit (TU) Kampen in April 2014, Vrije Universiteit (VU) Amsterdam in November 2014, and Theologische Universiteit (TU) Apeldoorn in April 2017. In 2014, the Bachelor of Theology Study Program received an accredited “B” rating by the National Accreditation Board for Higher Education (BAN-PT). And in 2015, the Master of Theology Study Program also received an accredited “B” rating. To improve research activities among the Christian universities, especially in the International Reformed Evangelical Seminary environment, the national journal Verbum Christi was published in 2014. Then, in 2015, the International Reformed Evangelical Seminary in collaboration with WTS published the International Journal of Reformed Theology and Life Unio Cum Christo to accommodate theological research activities globally. In January 2018, the Unio Cum Christo International Journal was indexed by the ATLA Religion Database.