The Council of churches in Zambia consists of the General Conference, which is the supreme body of the Council comprising member churches and affiliate organizations. The General conference is held once every three years at which elections are conducted to elect a ten-member executive Committee that acts on behalf of the General conference.

The General Secretary, who sits on the executive committee, heads the Secretariat.

The Secretariat, which comprises Administration/Finance and seven operational departments/programmes, is responsible for the day-to-day operation of the organisation.