Our study estimated the full economic cost of implementing performance-based financing [PBF, the Support for Service Delivery Integration Performance-Based Incentives (SSDI-PBI) programme], as a means of first introducing strategic purchasing in a low-income setting, Malawi. Our analysis distinguished design from implementation costs and traces costs across personnel and non-personnel cost categories over the 2012–15 period. The full cost of the SSDI-PBI programme amounted to USD 3 402 187, equivalent to USD 6.46 per targeted beneficiary. The design phase accounted for about one-third (USD 1 161 332) of the total costs, while the incentives (USD 1 140 436) represented about one-third of the total cost of the intervention and about half the cost of the implementation phase. With a cost of USD 1 605 178, personnel costs represented the dominant cost category. Our study indicated that the introduction of PBF entailed consumption of a substantial amount of resources, hence representing an important opportunity cost for the health system.