Purpose: This paper focuses on a classic optimization problem in operations research, the flexible job shop scheduling problem (FJSP), to discuss the method to deal with uncertainty in a manufacturing system. Design/methodology/approach: In this paper, condition based maintenance (CBM), a kind of preventive maintenance, is suggested to reduce unavailability of machines. Different to the simultaneous scheduling algorithm (SSA) used in the previous article (Neale & Cameron,1979), an inserting algorithm (IA) is applied, in which firstly a pre-schedule is obtained through heuristic algorithm and then maintenance tasks are inserted into the pre-schedule scheme. Findings: It is encouraging that a new better solution for an instance in benchmark of FJSP is obtained in this research. Moreover, factually SSA used in literature for solving normal FJSPPM (FJSP with PM) is not suitable for the dynamic FJSPPM. Through application in the benchmark of normal FJSPPM, it is found that although IA obtains inferior results compared to SSA used in literature, it performs much better in executing speed. Originality/value: Different to traditional scheduling of FJSP, uncertainty of machines is taken into account, which increases the complexity of the problem. An inserting algorithm (IA) is proposed to solve the dynamic scheduling problem. It is stated that the quality of the final result depends much on the quality of the pre-schedule obtained during the procedure of solving a normal FJSP. In order to find the best solution of FJSP, a comparative study of three heuristics is carried out, the integrated GA, ACO and ABC. In the comparative study, we find that GA performs best in the three heuristic algorithms. Meanwhile, a new better solution for an instance in benchmark of FJSP is obtained in this research.