The WECS is headed by Secretary, who is also the member secretary of the WEC. The WEC has four divisions: Energy, Water Resources, Legal and Administration, and Social and Environment. Each division is managed by Joint Secretary, who reports to the Secretary.

Water Resources Division:

The Water Resources Division has eight approved positions: within three sections: Hydropower, Irrigation and Basin Study. The Water Resources Division's function is to maintain data and analyze hydropower, irrigation and basin development studies in order to provide planning advice to the government. It provides policy and strategies for regional; and bilateral programs.

Energy Division:

The Energy Division has eight approved positions within three sections: Traditional Energy, Alternative Energy, and Commercial Energy. The Energy Division's function is to maintain data, provide liaison and formulate policy in relation to the supply and demand of indigenous and imported energy.

Social and Environment Division:

The Social and Environment Division has evolved from the integration of several divisions within the WECS. It is composed of three sections and five approved positions. The Social and Environment Division is an important resource to the Water Resources and Energy Divisions ensuring the issues such as gender, poverty, wealth creation, macro-economic analysis and environmental sustainability are integrated into water and energy policy development.

Legal and Administration Division:

The Legal and Administration Division is concerned with the legal and administration issues related to water and energy planning within the Government of Nepal, with the private sector and in with bilateral relations.