The scheduling problem in flexible manufacturing systems (FMS) environment with loop layout configuration has been shown to be a NP-hard problem. Moreover, the improvement and modification of the loop layout add to the difficulties in the production planning stage. The introduction of multi loading-unloading points and turntable shortcut resulted on more possible routes, thus increasing the complexity. This research addressed the reentrant FMS scheduling problem where jobs are allowed to reenter the system and revisit particular machines. The problem is to determine the optimal sequence of the jobs as well as the routing options. A modified genetic algorithm (GA) was proposed to generate the feasible solutions. The crowding distance-based substitution was incorporated to maintain the diversity of the population. A set of test was applied to compare the performance of the proposed approach with other methods. Further computational experiments were conducted to assess the significance of multi loading-unloading and shortcuts in reducing the makespan, mean flow time, and tardiness. The results highlighted that the proposed model was robust and effective in the scheduling problem for both small and large size problems.