The 19th Century A.D. is characterized by challenges of multiple levels that are associated with philosophical trends and modernistic currents and tendencies that cause intense crises not only to socio-economic structures; they also cause severe damage to the structural merit of institutions. The emergence of novel philosophical currents led to considerable controversy with regard to established positions and perceptions of Christianity in the West, which were reinforced by the activity of Protestant proselytism.

The Ecumenical Patriarchate, the venerable center of Orthodoxy, was a direct recipient of this challenge and the turbulence that was caused at the theological and inter-faith level. The key geopolitical position and function of the First See Church of Constantinople between the East and the West has made clear the need for the reconstruction of the intellectual powers of the Ecumenical Patriarchate. The creation of a scientific and intellectual staff center for the wholesome scientific training of its personnel was imperative. This prompted the establishment of the Theological School on the island of Halki of The Princes Islands.

Therefore, in the renovated Holy Monastery of the Holy Trinity, whose creation dates back to Byzantine times, under Patriarch Germanos 4th 1842-5), Metropolitan Paisios of Caesarea, blessed the inauguration of the Theological School of Halki in a separate ceremony, on 1st October 1844.

The building edifices of the Monastery were sufficient for the operating needs of the School. Unfortunately, however, the earthquake of 28th June 1894, was devastating, leaving behind most of the building structures in ruins.

Pavlos Skilitsis Stefanovik, a Greek of the Diaspora and benefactor of the Greek people, came to the financial aid of the School, responding to the Patriarchate's call; his monetary assistance helped rebuild the imposing building of the School. Its grand opening took place on 6th October 1896.

Since then, periodically and thus far, several remodeling interventions have taken place on the premises of the School along with upgrades of the equipment in order to meet its operating needs. Today, the School is fully ready to resume operation and can accommodate about 120 students.