Collaborative networks are complex systems and consist of many factors with dependencies among them. Although the number of collaborative networks such as advanced supply chains or virtual organizations/laboratories/e-science is growing and their significance is increasing in the world, many of them are unsuccessful. In addition, very little attention has been paid to the risk analysis of collaborative networks by considering the dependencies among risk factors. So, the precise risks analysis associated with collaborative networks projects is crucial to attain a satisfactory performance. To address this, we are proposing an advanced decision support tool called “Fuzzy Cognitive Maps” (FCM) which can deal with risks of such complicated systems by considering the interrelationships between factors. FCM states the behaviour of complex systems accurately and illustrate any complex environment based on the experts’ perceptions and by graphical representations. It is able to consider uncertainties, imprecise information, the interactions between risk factors, Information scarcity, and several decision maker’s opinions. FCM is not only able to evaluate risks more precisely in collaborative networks, but also it could be applied in different decision makings problems related to collaborative networks such as partner selection and forecasting behaviors, policy analysis, modeling collaboration preparedness assessment, etc. Hence, the proposed tool would help practitioners to manage collaborative network risks and decision making problems effectively and proactively.