FAPESP's Board of Trustees (CS) is responsible for the Foundation's general management and for the strategic decisions concerning its science, technology, administrative and asset policies. Each one of its twelve members has a six-year term of office. Six members are freely chosen by the State Governor. The other six are chosen by the Governor, each one from a list of three nominees appointed by the São Paulo science and technology community.

The Chairman of the Foundation, who is chosen from amongst the Board members, is also the chairman of the CS and FAPESP's legal representative.

The Executive Board (CTA) consists of the President Director, the Scientific Director and the Administrative Director, each of them with a three-years term of office, chosen by the Governor, from a list of three nominees submitted by the Board Trustees.