Abstract Similar to other energy systems, economic analysis of cogeneration systems is one of the most important steps in their design procedure. In this paper, a novel method is suggested for economic optimization of cogeneration systems. This method provides an opportunity to consider uncertainties in various economic parameters. Accordingly, by providing the probability distribution function of the net present value or payback time, this method offers further insights in economic evaluations of cogeneration systems. As a common practice for demonstrating novel methodologies in design and optimization of cogeneration systems, the proposed method of this study is applied to a well-known cogeneration case in the literature. In a coupled scheme, Monte Carlo approach is applied with net present value method to optimize the system. Accordingly, the obtained result is the probability distribution function of the net present value of the maximum profit. The results verify that compared to previously used methods which did not consider uncertainties in economic parameters, this probability distribution function provides a more general point of view on the profitability of the system. Therefore, by showing economic risks, these considerations make investments in this cogeneration system far more interesting.