To guide the Ministry of Health in Ghana in the priority setting of interventions by quantifying the trade‐off between equity, efficiency, and other societal concerns in health. The study applied a multicriteria decision analytical framework. A focus group of seven policymakers identified the relevant criteria for priority setting and 63 policymakers participated in a discrete choice experiment to weigh their relative importance. Regression analysis was used to rank order a set of health interventions on the basis of these criteria and associated weights. Policymakers in Ghana consider targeting of vulnerable populations and cost‐effectiveness as the most important criteria for priority setting of interventions, followed by severity of disease, number of beneficiaries, and diseases of the poor. This translates into a general preference for interventions in child health, reproductive health, and communicable diseases. Study results correspond with the overall vision of the Ministry of Health in Ghana, and are instrumental in the assessment of present and future investments in health. Multicriteria decision analysis contributes to transparency and accountability in policymaking.