The foundation of the Bitola Seminary was to a great extent possible due to efforts of Bishop Josif Cvijović (1878–1957), so its fate was tied to him. The idea to open a seminary arose shortly after his enthronement, in the summer of 1921. The seminary was built in very difficult conditions because Bitola, as a border town on the outskirts of the Kingdom of Serbs, Croats and Slovenes, was largely destroyed and devastated. On the other hand, there was a lack of material resources because opening this new school was not foreseen in the state budget. Bishop Josif, in his efforts to open a seminary, was extremely supported by the then Bishop Nicholai of Ohrid.

Bishop Nicholai Velimirovich (1881–1956) has supported the Bitola Theological Seminary since the efforts to establish this seminary in 1921. In order to enable the opening of the Bitola Theological Seminary, the collecting of contributions in money and things for the basic needs of the school and boarding school has begun in 1921. The American Commission to Serbia (Commissioner Dr. Rudolph Rex Reeder (1859–1934)) was the first to send abundant aid, thanks to Bishop Nicholai Velimirovich who interceded with the scientist Mihajlo Pupin (1854–1935) on this issue. As the diocesan bishop of the Diocese of Ohrid and Bitola, Bishop Nicholai took special care of the Seminary of St. John the Theologian in Bitola in the period from 1932 until 1938, when he moved to the Diocese of Žiča.