The urban rail system in Istanbul carries in total more than 700.000 passengers per a day on different types of lines which require well organized risk governance. This paper evaluates the urban rail systems in Istanbul under different risk factors using Fuzzy Analytic Hierarchy Process (FAHP) to uncover the critical risk criteria of these systems and to make a multi-criteria evaluation of existing rail systems for the assignment of the scarce resources. Linguistic variables are used in the pairwise comparisons of criteria and alternatives. The risk factors considered are regional criticality, line characteristics, line safety and station structure. The evaluation results imply that the most risky critical urban rail system in Istanbul is the subway line from Sishane to Darussafaka.