Job sequencing is an important stage in any hierarchical production control model, especially when a real‐time dispatching rule is not employed. The problems become complicated when constraints, such as different parts requiring different operation processes at different machines and with different production priorities, are taken into consideration in the development of sequencing models. This paper first describes a mathematical programming model developed for small flexible manufacturing systems (FMS) makespan minimization sequencing problems. For large problems, a heuristic decomposition‐based algorithm is proposed. The algorithm is based on the proposed concept of track generation and track identification. Each part type may require a different number of operation processes at different machines. A numerical example is used to illustrate the use of the algorithm.