The [[seminary]] was housed on the site of the ruined [[Monastery of the Holy Trinity]], which was founded by [[Photius I]], [[Patriarch of Constantinople]] (r. 858–861 and 878–886). In 1844, Patriarch [[Germanos IV]] converted the ruined monastery into a school of theology, which was inaugurated on September 23, 1844. All the buildings except for the chapel were destroyed by an earthquake in June 1894, but were rebuilt by architect Periklis Fotiadis and inaugurated in October 1896. Major renovation took place in the 1950s.

The theological facilities include the [[Chapel of the Holy Trinity]], sports and recreational institutions, dormitories, an infirmary, a hospice, offices, and the school's library with its historic collection of books, journals, and manuscripts. The students at Halki included not only a large number of native born Greeks, but Orthodox Christians from around the world, giving the school an international character.