Rapid shifts in consumer preferences have prompted enterprises to offer products in small quantities and various options. To meet market demands, enterprises must be able to research the development of modern conceptions of manufacturing systems which has revolved around new practical and scientific results that are able to meet the assumptions of focused flexible manufacturing systems (FMSs) and the challenges of the Industry 4.0 philosophy. These FMSs, which incorporate automated facilities and computer control systems, play a crucial role in boosting the productivity of enterprises. In this study, the development trajectory and applications of FMS research were investigated. Scopus was used to collect and organize voluminous data, and main path analysis was used to identify the most relevant studies on FMS research. The results revealed that early FMS research concentrated on fundamental property analysis. After the flexibility and productivity of these systems were enhanced, the elimination of loading problems was discussed. Generally, FMS research has emphasized factor identification, flexibility evaluation, pre-simulation, and optimization. In this study, cluster analysis was used to identify five subfields: loading problem mitigation through scheduling, decision-making facilitation through simulation, FMS deadlock prevention, FMS flexibility measurement, and FMS composition. This study provides planning directions for industry, and the findings serve as a reference for manufacturing systems. The integrated analysis successfully determined the trajectory of FMS based technological development and applications as well as forecast the direction of future research.