This paper elaborates on the application of Fuzzy Cognitive Maps (FCMs) in strategy maps (SMs). The limitations of the Balanced Scorecards (BSCs) and SMs are first discussed and analyzed. The need for simulated scenario based SMs is discussed and the use of FCMs as one of the best alternatives is presented. A software tool for the development, simulation and analysis of FCM based SMs is also presented. The effectiveness of the resulting software tool and FCM theory in SMs is experimented in two case studies in Banking