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, and South Asia that are hosted by a local university.

J-PAL's Programs include Agriculture, Education, Energy and Environment, 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 3 members, who, along with J-PAL Global Directors and J-PAL's Global Director of Policy 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.