Reformed Church of Nepal has two governance structures. One deals with ecclesiastical matters such as doctrine, ethical issues, and church life and practice. The second is in place to govern the ministries undertaken jointly by RCN congregations.

Ecclesiastical Governance
The ecclesiastical structure involves the church assemblies: the council (local assembly), the classis (regional assembly), and the synod.

The ecclesiastical structure is as follows:

Note: We speak of our major assemblies as broader, not higher, assemblies. Therefore, the grid is horizontal, not vertical.

Ministry Governance
Although the synod maintains general oversight of RCN ministries, it has created a system of boards to govern individual ministries (agencies). Currently we are developing several boards, each governing a different ministry, with authority to make the necessary decisions for their agencies.

In addition to these boards, another board will be established with the authority to supervise the management of the agencies and committees established by synod, including the planning, coordinating, and integrating of their work. This board is known as the Board of Trustees of Reformed Church of Nepal. It will operates as an agent of synod and reports yearly to synod on its work. The position of executive director and the ministry council are also important parts of the RCN's governance structure.

The complete governance schematic is as follows: