The relationship between a government and a franchise firm in a build-operate-transfer (BOT) project is one that is wrought with incentive problems. It is well known that a contingent payment structure can help alleviate moral hazard problems. This paper provides a flexible franchise fee scheme from the perspective of a government which can charge a sufficient franchise fee and provide enough incentive for a private firm in a BOT project. This flexible franchise fee structure has option-like properties. A pricing model is derived in this paper to price this flexible franchise fee scheme. The closed-form pricing model that I have provided in this paper can help evaluate the effect of a flexible franchise fee on the performance of BOT projects. A numerical analysis shows that the proposed flexible franchise fee scheme is especially suitable for BOT projects with long investment horizons and revenue uncertainty.