The Great Kanto earthquake of 1923 caused a set back for the seminary as for the whole Church as all the main buildings of the Kanda Suragadai complex were destroyed or seriously damaged, including the library that held over 30,000 volumes. Abp. Sergius and the Japanese Church not only had to rebuild the Holy Resurrection Cathedral (Nicolai-do) but the administrative facilities also, including the seminary, with only resources of the Japanese Church to accomplish this work. After recovering from this catastrophe the Church and its seminary were disrupted again by World War II and its aftermath. The seminary was closed for most of the 1940s and early 1950s until it was reopened by [[Ireney (Bekish) of New York|Bp. Ireney]] in 1954, after he assumed leadership of the Church of Japan. As part of the recovery the Church and Seminary began again publishing Bibles and theological books as well as sending graduates of the Tokyo Seminary to the seminaries in the United States for advanced studies, specially until 1970s.

Currently it accepts only Orthodox faithfuls over eighteen and provides them three years theological education. The minimum requirement of their educational level for entrance is that they finished high school, however students are basically expected to be already graduated in a secular university. Today, the Tokyo Seminary continues to grow and continue on its path to the excellence it possessed during the turn over of the nineteenth and twentieth centuries.