The Pugwash Conferences have a loose organizational structure. the President of the Pugwash Joseph Rotblat is the titular head of the organization; the Secretary-General (since 1989 Francesco Calogero, Professor of Theoretical Physics at the University of Rome "La Sapienza") has the overall executive responsibility; formal governance of the organization is by a (currently 23 - member) Council (which generally meets once a year and is elected every five years at the "Quinquennial" Conferences, held since 1962, which lay out the goals of the Pugwash) and its 10 - member Executive Committee (which meets once or twice a year). International arrangements and communication are coordinate through three small permanent offices in London (in front of the British Museum), Geneva (near the United Nations), and Rome (in the National Academy of the Lincei -- "Accademia Nazionale dei Lincei"), which operate with a total of three staff persons (plus six conscientious objectors in the Rome office). Over 30 National Pugwash Groups -- organized independently, and in several cases sponsored and/or administered by academies of sciences -- help to identify suitable participants from their countries and rotate the work of hosting meetings (with funds raised locally). There are approximately 12 Student / Young Pugwash Groups.

Costs of operating the Pugwash offices in Geneva, London and Rome are met by a combination of donated services, and contributions from individuals, foundations, and National Pugwash Groups (in proportion to their participation and ability to pay: for instance, the largest contribution, by the U.S. Pugwash Group, now amounts to US$ 25,000 per year). Costs of participant's food and lodging during meetings are generally covered by the host Pugwash Group, with participants providing their own travel funds from foundations and individuals, and in some instances from their governments (often through national academies of sciences). No honoraria or other fees are paid to participants in Pugwash meetings, nor to the officers of Pugwash (who serve voluntary -- unremunerated -- basis).