In a flexible manufacturing system (FMS) scheduling problems become extremely complex, even for simple breakdowns, when dynamic uncertainties such as machine breakdowns and the uncertain arrival of jobs are taken into consideration. In the first stage of this study, a fuzzy logic-based algorithm for assigning priorities to part types that are to be machined is proposed. In the second stage, an operation-machine allocation and scheduling algorithm is presented. A criteria contribution equalizer is used in decision-making. The proposed algorithm can re-generate the schedule in case of a machine breakdown, and therefore can be used as an on-line controller. The system architecture and linguistic variables are presented and results showed that the proposed algorithm improves the system efficiency.