The Assyrian Church of the East is led by the Catholicos-Patriarch of the East (also called the Nestorian Patriarch), who is the supreme ecclesiastical authority of the autonomous church. The church traces its apostolic succession to the Apostles Thomas, Addai, and Mari, who are believed to have brought Christianity to Mesopotamia and the East. This distinctive apostolic lineage—separate from both the Petrine succession of Rome and the Alexandrian succession of the Eastern Orthodox—is a fundamental component of the church's identity.

The church is organized episcopally, with bishops, priests, and deacons. No papal authority or subordination to Rome or to the Ecumenical Patriarch of Constantinople is recognized. The church maintains its autonomy and ancient traditions, seeing itself as the direct continuation of the Apostolic church in the East. Authority is exercised through the Catholicos-Patriarch in consultation with the church's leadership and councils. The church's doctrinal authority derives from Scripture, the Apostolic Tradition as expressed in the early Councils, and the patristic and liturgical tradition of the East Syrian church.