NTO membership is voluntary. The main governing bodies of the NTO are the NTO Assembly, the NTO Council, the Head of Council, the Focal Points, the Working Groups, and the NTO Secretariat. 

The NTO Secretariat is member-led with support from the International Tax Compact (ITC), which is funded by the German Federal Ministry for Economic Cooperation and Development (BMZ) and co-funded by  the European Union. The ITC is implemented by the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH.

The NTO activities are supported by the ITC and are also funded through the in-kind contributions of its members.