The Presbyterian Church (U.S.A)'s local governing body is the Session. Each church associated with the Presbyterian Church (U.S.A) has a Session that oversees and coordinates the operations of the church.

The Session of Church of the New Covenant consists of 9 Ruling Elders plus the pastor, who serves as moderator. There are three classes of three elders. Each elder serves for three years. Church of the New Covenant has a tradition of including youth in the government of the church. Every year the church elects a Youth Elder, who serves a term of one year.