The present paper considers possibilities for managing effectiveness of enterprise e-business system by the use of a specially developed software tool. The software is developed based on the self-established ontological model describing the area of the enterprise e-business system and methodology for assessment and management of the efficiency of this system. Opportunities for application of the developed tool include its usage by senior executives at the stage of developing a strategy for e-business of the company or evaluation of the existing enterprise e-business system. In the last case, the software would help optimise these systems.