Objectives. To document the underlying science of how the Pan American Health Organization (PAHO) adapted the Hanlon method, which prioritizes disease control programs, to its wider range of program areas and used it to implement the PAHO Strategic Plan 2014 – 2019. Methods. In 2014, PAHO established a Strategic Plan Advisory Group (SPAG) with representatives from 12 Member States to work closely with the PAHO Technical Team to adapt the Hanlon method to disease and non-disease control programs. Three meetings were held in 2015 – 2016 during which SPAG reviewed existing priority-setting methods, assessed the original Hanlon method and subsequent revisions, and developed the adapted method. This project was initiated by Member States, facilitated by PAHO, and conducted jointly in transparent and horizontal technical cooperation. Results. From the original Hanlon equation, the PAHO-adapted method maintains components A (size of problem), B (seriousness of problem), and C (effectiveness of intervention), drops component D (PEARL – Propriety, Economics, Acceptability, Resources, and Legality), and adds component E (inequity) and F (institutional positioning). The PEARL score was dropped because it serves a purpose for pre-screening process, but not in the priority-setting process for PAHO. Conclusions. The PAHO-adapted Hanlon method provides a refined approach for prioritizing public health programs that include disease and non-disease control areas. The method may be useful for the World Health Organization and country governments with similar needs.