Prathinidhi Sabha (Representative Assembly) is the supreme authority of the Church in all spiritual and temporal matters. The President Adhyashkan of the Prathinidhi Sabha is elected by the members of the Prathinidhi Sabha. The individual need not be a Bishop, both the President and the Vice President can be laymen. The members of the Prathinidhi Sabha are elected from each parish, one or two individuals, for every 50 families in each parish. The members also include all Presbyters and Bishops of the Church. Elections for the Prathinidhi Sabha members are held every three years.

All Organizations, Dignitaries, various Committees in the Church will have only such power as the Prathinidhi Sabha confers upon them. The President of the Prathinidhi Sabha is not the President of the Church. The President of the Church, Presiding Bishop, is elected by the Prathinidhi Sabha for every five years from among the Senior most Bishops of the Church. The Bishop can serve only two terms as Presiding Bishop of the Church, with five years for each term continuously.

The first Prathinidhi Sabha was held on January 26, 1961 by Presiding Bishop K. N. Oommen.