Jerusalem Mar Thoma Church is led by a Vicar and two Assistant Vicars. The general body, also called the Edavaka Sangham, comprising all the adult members of the church, is the supreme decison making body of the parish. The day-to-day administration of the church is handled by an Executive Committee headed by the President who is the Vicar and two clergy Vice Presidents along with elected Lay Vice Presidents, Secretary, Trustees, Lay Ministrants and the area and organizational Representatives. The annual accounts and budget of the parish are cleared by the Edavaka Sanghom. The Executive Committee is also called the Kaisthana Samithi.

For administrative convenience and fellowship, the parish is divided into prayer groups arranged geographically and have representatives to the Kaisthana Samithi. The Executive Committee has a tenure of one year and runs coterminous to the Financial year of the Governemt of India.

The Executive Committee members elected for the year 2026-2027 are given below: