The article reviews the prerequisites to use real options in the design of information systems (IS) as a variety of investment designing. On the one hand, these presuppositions include the risk and uncertainty in the long process of designing and, on the other hand, the possibility to demonstrate the managerial flexibility of the project manager. The main factors of uncertainty and risk include the functionality of IS, requirements to which are approximately formulated by the customer, and then are necessary to be clarified at every stage of the design in accordance with the changing circumstances and the project financing possibilities. The assessment methods of real options such as the Black–Scholes model, binary tree, etc. require initial data that are difficult and even impossible to obtain while designing enterprise information system due to the insufficiency of statistics that characterize the cash flows of such projects. Furthermore, these models ignore the features of the IS design that could be reflected in an optional approach to design. The features of the optional approach to IS design are analyzed and summarized in four groups: 1) factors of uncertainty and risk; 2) the variant approach to design; 3) staging of the design process; 4) the iterative nature of the design process. The classification of types of real options in the design process is proposed. The factors of management flexibility by design stages and types of real options are analyzed. The work offers a consistent economic efficiency assessment of IS based on the expected values of the expanded net present value of the project that are confirmed at every stage of the design. The formula of the expected value of the cost of a real option for binary development of the design process is proposed. The use of real options in the information system design, taking into account the peculiarities of this process, makes it possible to improve the economic efficiency of the project and its attractiveness.