The church was established in 1924, to accommodate Orthodox Christians of Polish descent in the eastern part of the country, when Poland regained its independence after the First World War.

[2] Following the partitions of Poland and the annexation of Polish territory by the Russian Empire, the administration of Eastern Orthodox communities was carried out by the vicar bishop of Pereyaslav and Boryspil of the Kyiv Eparchy with residence in Slutsk.

Following the 1905 revolution in the Imperial Russia, Tsar issued the manifest "On strengthening the principles of religious tolerance" which gave start to revival of Catholicism.

[6] Following the 1917–18 Local Council of the Russian Orthodox Church, Patriarch Tikhon of Moscow finally appointed a new bishop to the eparchy of Warsaw who was Seraphim (Chichagov).

The loss of an ecclesiastical link, due to the persecution of the Russian Orthodox Church in the Soviet Union, left the regional clergy in a crisis, and in 1924 the Ecumenical Patriarchate took over, establishing several autonomous churches on territories of the new states that were formerly wholly or partially part of the Russian Empire: Finland, the Baltic states, and Poland.

[7] In 1922 a conflict ensued due intervention of the Russian Orthodox Church that approved appointment of bishops in Poland without agreement from Metropolitan of Warsaw George (Yaroshevsky).

[8] Several diocesan bishops along with Eleftherios of Wilno including Panteleimon (Rozhnovsky), Vladimir (Tikhonitsky) and others took stance against seeking autocephalous status for the Orthodox Church in Poland.

[9] Earlier, in January 1922, the Polish government had issued an order recognizing the Orthodox church and placing it under the authority of the state.

[10] Nonetheless, his successor, Dionizy (Waledyński), continued to work for the autocephaly of the Polish Orthodox church, which was finally granted by the Ecumenical Patriarch of Constantinople in his Tomos of 13 November 1924.

[15] At the end of 1940, Metropolitan Dionisius signed a loyalty declaration for the General Governor of Poland Hans Frank and was released from his arrest.

After the Second World War, the pre-war eastern territories of Poland were annexed by the Soviet Union and included within the Lithuanian, Byelorussian and Ukrainian SSRs.

[10][16] Although most of the congregation is historically centered in the Eastern borderland regions with considerable Belarusian and Ukrainian minorities, there are now many parishes across the country, as a result of Operation Vistula and other diaspora movements.

[17][19] In 2003, following the decision of the Holy Sobor of Bishops of the Polish Autocephalous Orthodox Church, the New Martyrs of Chelm and Podlasie suffering persecution during the 1940s were canonized.