The university traces its origin to 1894, when eight congregations of the Christelijke Gereformeerde Kerken gathered for their first national synod and resolved to train their own pastors. The Christian Reformed Churches had broken from the Dutch state church a generation earlier in the Afscheiding of 1834, a small revolt of conservative believers who felt the established church had drifted from its confessions. The new federation needed its own seminary, and in 1894 it opened one in The Hague. In 1919 the school moved east, to Apeldoorn - a quieter Reformed stronghold on the Veluwe - where it has remained ever since. The campus is modest and unmarked. The library, however, is serious.

The TUA program is structured as a three-year bachelor followed by a three-year master, with biblical languages front-loaded and dogmatics, church history, ethics, apologetics, and church law layered on top. The school is also licensed to grant a doctorate in theology, a right it has held since 1980. The intent is unapologetically vocational: most students arrive expecting to be ordained. Yet since 1968 the doors have opened to anyone wanting serious theological training, and the student body now includes Koreans, Indonesians, and other international students drawn to the school's reputation for rigorous Reformed scholarship. A minority of graduates actually end up in CGK pulpits - the federation is small, and pulpits are few - so the training has had to prepare ministers for export as well.

TUA partners with the Theological University of the Reformed Churches in Utrecht on a combined research program called BEST - Biblical Exegesis and Systematic Theology - which deliberately bridges two disciplines that often grow apart. Old Testament scholars and dogmaticians rarely share a corridor; the BEST program puts them in the same room. Across the Atlantic, the university teamed up with the Puritan Reformed Theological Seminary in Grand Rapids, Michigan in 2017 to launch a joint Puritan research center and a combined doctoral track. A more ambitious 2017 plan would have merged TUA with the Reformed seminary in Kampen and the Netherlands Reformed ministerial program into a single national Reformed university; the Christelijke Gereformeerde synod rejected it, preferring the independence the small school has always defended.

In September 2021 the university launched a new master's program called Living Reformed Theology, a 60 EC degree designed to be taken part-time or on a faster track. The interdisciplinary framing pushes Old Testament study into conversation with practical theology, dogmatics into conversation with church polity. The program reflects what TUA has been doing on a smaller scale for decades: training pastors who can read Hebrew and Greek but also stand in a Dutch pulpit on a Sunday morning and explain why any of it matters in the present tense. The institution remains tiny by global university standards. By the standards of its own tradition, it is the central place where that tradition thinks.