Background Overweight and obesity are major risk factors for noncommunicable diseases. This presents a major burden to health systems and to society in South Africa. Collectively, these conditions are overwhelming public healthcare. This is happening when the country has embarked on a journey to universal health coverage, hence the need to estimate the cost of overweight and obesity. Our objective was to estimate the healthcare cost associated with treatment of weight-related conditions from the perspective of the South African public sector payer. Using a bottom-up gross costing approach, this study draws data from multiple sources to estimate the direct healthcare cost of overweight and obesity in South Africa. Population Attributable Fractions (PAF) were calculated and multiplied by each disease’s total treatment cost to apportion costs to overweight and obesity. Annual costs were estimated for 2020.Results The total cost of overweight and obesity is estimated to be ZAR33,194 million in 2020. This represents 15.38\% of government health expenditure and is equivalent to 0.67\% of GDP. Annual per person cost of overweight and obesity is ZAR2,769. The overweight and obesity cost is disaggregated as follows: cancers (ZAR352 million), cardiovascular diseases (ZAR8,874 million), diabetes (ZAR19,861 million), musculoskeletal disorders (ZAR3,353 million), respiratory diseases (ZAR360 million) and digestive diseases (ZAR395 million). Sensitivity analyses show that the total overweight and obesity cost is between ZAR30,369 million and ZAR36,207 million. This analysis has demonstrated that overweight and obesity impose a huge financial burden on the public health care system in South Africa. It suggests an urgent need for preventive, population-level interventions to reduce overweight and obesity rates. The reduction will lower the incidence, prevalence, and healthcare spending on noncommunicable diseases.