The JEMB Secretariat implements election operations from HQ in Kabul, eight regional offices, and 34 provincial offices (plus two sub-offices).

The Chief and Deputy Chief Electoral Officers head the JEMB Secretariat organizational structure. The Management Office, consisting of the Chief of Operations and the Chief of Staff underneath the Chief Electoral Officer, assume responsibility for the day-to-day management and coordination of a flat structure of Departments. The Chief of Operations ensures that all departments and offices implement the operational plan according to the budget and timeline. The Chief of Staff ensures that the resources necessary to conduct the operation are in place and that the organization runs efficiently to implement the operation.

The JEMB Secretariat Departments are External Relations, Legal Services and JEMB Support, Public Outreach, Support, Program Management, Communications and IT, Security, Training and Capacity Building, and Field Operations. Heads of Department report to the Management Office. All operational issues are managed by the Chief of Operations, while all resource issues are managed by Chief of Staff.