The WECS is headed by secretary, who is also the member secretary of the WEC . The WEC has four divisions Energy Planning, Water Resources, Legal and Institutional Arrangement, and Social, Economic and Environment. Each divisions is managed by joint secretary, who reports to the secretary.

Water Resources Division

The Water Resources Division has eight approved positions within three sections: Hydro power, irrigations 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 Planning Division

The Energy Planning Division has eight approved positions within three sections: Traditional Energy, Alternative Energy, and Commercial Energy. The Energy planning 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, Economic and Environment Division (SEED)

The SEED has evolved from the integration of several Divisions within the WECS. It is composed of three sections and five approved positions. The SEED is an important resource to the Water Resources and Energy Planning 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 Institutional Arrangement Division (LID)

The LID is concerned with the legal, institutional and regulatory issues related to water and energy planning within the government of Nepal, with the private sector and in with bilateral relations.