The Orthodox Bulgarian National Church claims to be an indivisible member of the Eastern Orthodox communion, and asserts historic continuity with the autocephalous Bulgarian church of the middle ages. It was, however, declared schismatic by the Greek patriarch of Constantinople in 1872, although differing in no point of doctrine from the Greek Church. The Exarch, or supreme head of the Bulgarian Church, resides at Constantinople; he enjoys the title of "Beatitude" (negovo Blazhenstvo), receives an annual subvention of about £6000 from the kingdom, and exercises jurisdiction over the Bulgarian hierarchy in all parts of the Ottoman empire. The exarch is elected by the Bulgarian episcopate, the Holy Synod, and a general assembly (obshti sbor), in which the laity is represented; their choice, before the declaration of Bulgarian independence, was subject to the sultan's approval. The occupant of the dignity is titular metropolitan of a Bulgarian diocese. The organization of the church within the principality was regulated by statute in 1883. There are eleven eparchies or dioceses in the country, each administered by a metropolitan with a diocesan council; one diocese has also a suffragan bishop.

Church government is vested in the Holy Synod, consisting of four metropolitans, which assembles once a year. The laity take part in the election of metropolitans and parish priests, only the "black clergy," or monks, being eligible for the episcopate. All ecclesiastical appointments are subject to the approval of the government. There are 2106 parishes (eporii) in the kingdom with 9 archimandrites, 1936 parish priests and 21 deacons, 78 monasteries with 184 monks, and 12 convents with 346 nuns. The celebrated monastery of Rila possesses a vast estate in the Rilska Planina; its abbot or hegumen owns no spiritual superior but the exarch. Ecclesiastical affairs are under the control of the minister of public worship; the clergy of all denominations are paid by the state, being free, however, to accept fees for baptisms, marriages, burials, the administering of oaths, etc. The census of January 1901 gives 3,019,999 persons of the Orthodox faith (including 66,635 Patriarchist Greeks), 643,300 Mahommedans, 33,663 Jews, 28,569 Catholics, 13,809 Gregorian Armenians, 4524 Protestants and 419 whose religion is not stated. The Greek Orthodox community has four metropolitans dependent on the patriarchate.

The Mahommedan community is rapidly diminishing; it is organized under 16 muftis who with their assistants receive a subvention from the government. The Catholics, who have two bishops, are for the most part the descendants of the medieval Paulicians; they are especially numerous in the neighbourhood of Philippopolis and Sistova. The Armenians have one bishop. The Protestants are mostly Methodists; since 1857 Bulgaria has been a special field of activity for American Methodist missionaries, who have established an important school at Samakov. The Berlin Treaty (Art. V.) forbade religious disabilities in regard to the enjoyment of civil and political rights, and guaranteed the free exercise of all religions.