Objectives: Busan had the highest mortality and the shortest life expectancy at birth among 16 provinces in Korea in 2008 and there were considerable health inequalities within the region. This study was performed to build up a priority setting framework in Healthy City Busan project. Methods: Analytic hierarchy process was used to determine the relative priority weight for different strategic and program dimensions along with the consistency of response. An on-site workshop-based meeting (calculating importance) and online survey (calculating risk) were conducted to obtain data from 8 experts. Results: The results showed that in strategic criteria "active health promotion & diseases prevention" and "building infrastructure for the Health City project" were two most important factors. In program criteria, considering both importance and risk scores, "making a healthy community" and "building community health centers" in disadvantaged areas were a top priority group. In addition, "enacting an ordinance for the Healthy City", "building the infrastructure for health impact assessment" and "making health care safety net for vulnerable population" were also higher priorities group. Conclusions: Our findings suggest that the Healthy City project in Busan should be focused on strengthening health equity and building infrastructure for sustainability of the project.