The structure of the Christian Methodist Episcopal Church includes general or connectional ministries and operations to promote the needs and interests of the denomination. These ministries and operations are known as Departments and are headed by General Secretaries.

During the interim of the General Conference, each department reports annually to the General Connectional Board regarding the conduct and administration of their respective offices.

Each connectional department is designed to administer to local congregations and the church and has a standing committee which consists of both lay and clergy representatives from the respective Episcopal Districts.

The departments are divided into Connectional Ministries and Connectional Operations. Connectional Ministries are those departments that are designed to minister directly to the local congregations, district conferences, and annual conferences. Thus, these ministries exist on all levels of the Church. The Connectional Ministries Programmatic Departments are Christian Education, Lay, Evangelism and Missions, and Communication and Information Technology.

The Connectional Operations departments are designed to serve the Church at the Connectional level and keep the denomination operational. These departments are Finance, Publications and Personnel Services.