The article deals with the development of the control procedures support system (CPSS) of an investment project in the fuel and energy complex (FEC) based on the use of intelligent technologies. The stages of management of investment projects in a particular fuel and energy company are presented. The estimation of deviations of the actual performance indicators of the project from the planned is presented, the conclusion about the need to use intelligent algorithms of decision-making support in order to reduce risks under uncertainty is made. An approach to solve the problem of development of CPSS of the investment project in the enterprise is proposed. The procedure of neural network data analysis and decisionmaking in the management of the investment project based on the construction of self-organizing Kohonen maps is developed. The examples of the pessimistic and realistic scenarios for managing the implementation of the investment project are presented. It is shown that the timeliness and the correctly chosen sequence of decision-making in time allow for obtaining greater profits, and therefore, achieving the stability in the functioning of the main and investment production and after the completion of the investment project. The developed CPSS of the investment project can be applied at the level of heads of the enterprises as an adviser in the implementation of scenario approach in the management of real investment projects.