J-PAL is organized both by regional offices and by research themes called Programs. J-PAL's headquarters is a center within the Economics Department of the Massachusetts Institute of Technology (MIT), with regional offices in Africa, Europe, Latin America & Caribbean, North America, South Asia, and Southeast Asia that are hosted by a local university.

J-PAL's Programs include Agriculture, Education, Environment and Energy, Finance, Health, Labor Markets, and Political Economy and Governance. These regional offices and Programs are directed by members of the J-PAL Board, which is composed of J-PAL affiliates and senior management. However, J-PAL's affiliate professors set their own research agenda and raise funds to support their evaluations.

The Board of Directors provides overall strategic guidance to J-PAL and helps expand activities in research, capacity building, and policy outreach. The Board elects three members, who, along with the J-PAL Directors and Deputy Director, form an Executive Committee that meets on a more frequent basis on decisions that have bearings on the direction of J-PAL and provide guidance and oversight to J-PAL's staff worldwide.