Foot-and-mouth disease (FMD) prevention and control is a challenge worldwide but the situation in southern Africa is particularly complex because the virus is endemic in wild African buffalo (Syncerus caffer). The objective of this study was to compare stakeholder perceptions of the FMD control methods employed to restrict FMD virus to the infected zone of South Africa. Data collection was performed using an online questionnaire distributed to FMD experts, government veterinarians, private livestock veterinarians, people involved within the wildlife sector, and "other" occupation groups including the general public. Data were also collected using semi-structured participatory group discussions with government animal health technicians (AHT) and communal cattle owners directly affected by FMD control measures. Evaluated control methods were the disease control fence bordering the western boundary of the Greater Limpopo Transfrontier Conservation Area, clinical surveillance of livestock, movement control of cloven-hoofed animals and products, and routine FMD vaccination of cattle. These management procedures were scored according to a set of technical, economic, and ethical criteria by stakeholders, who also weighted the criteria according to their perceived importance. Scores and weights were aggregated using an additive linear model to rank control methods. Sensitivity analysis was performed using a stochastic model to explore the effects of varying inputs and the exclusion of scores from randomly selected respondent groups on the ranking of control methods. The deterministic analysis assigned the highest ranking to the disease control fence and the lowest to routine vaccination of cattle. The fence had the highest ranking in 40% of the stochastic iterations, and second, third and fourth in 26%, 20% and 14% of iterations, respectively. The inputs from the AHT and people involved in the wildlife sector were the most influential for ranking the fence as the preferred control option. The most influential criteria were the feasibility of the fence as a control option and its influence on the economics of the communal cattle owners, livestock industry in the FMD free zone, and the government. The disease control fence was the highest ranking control option but further investigations are necessary to understand the reasons for stakeholder perceptions.