Sustainable traffic system management under conditions of uncertainty and inappropriate road infrastructure is a responsible and complex task. In Bosnia and Herzegovina (BiH), there is a large number of level crossings which represent potentially risky places in traffic. The current state of level crossings in BiH is a problem of the greatest interest for the railway and a generator of accidents. Accordingly, it is necessary to identify the places that are currently a priority for the adoption of measures and traffic control in order to achieve sustainability of the whole system. In this paper, the Šamac–Doboj railway section and passive level crossings have been considered. Fifteen different criteria were formed and divided into three main groups: safety criteria, road exploitation characteristics, and railway exploitation characteristics. A novel integrated fuzzy FUCOM (full consistency method)—fuzzy PIPRECIA (pivot pairwise relative criteria importance assessment) model was formed to determine the significance of the criteria. When calculating the weight values of the main criteria, the fuzzy Heronian mean operator was used for their averaging. The evaluation of level crossings was performed using fuzzy MARCOS (measurement of alternatives and ranking according to compromise solution). An original integrated fuzzy FUCOM–Fuzzy PIPRECIA–Fuzzy MARCOS model was created as the main contribution of the paper. The results showed that level crossings 42 + 690 (LC4) and LC8 (82 + 291) are the safest considering all 15 criteria. The verification of the results was performed through four phases of sensitivity analysis: resizing of an initial fuzzy matrix, comparative analysis with other fuzzy approaches, simulations of criterion weight values, and calculation of Spearman’s correlation coefficient (SCC). Finally, measures for the sustainable performance of the railway system were proposed.