Flexible Manufacturing Systems (FMSs) provide a competitive edge in the ever-evolving manufacturing landscape, offering the agility to swiftly adapt to changing customer demands and product lifecycles. Nevertheless, the complex and interconnected nature of FMSs presents a distinct challenge: the evaluation and prioritization of performance variables. This study clarifies a conspicuous research gap by introducing a pioneering approach to evaluating and ranking FMS performance variables. The Best-Worst Method (BWM), a multicriteria decision-making (MCDM) approach, is employed to tackle this challenge. Notably, the BWM excels at resolving intricate issues with limited pairwise comparisons, making it an innovative tool in this context. To implement the BWM, a comprehensive survey of FMS experts from the German manufacturing industry was conducted. The survey, which contained 34 key performance variables identified through an exhaustive literature review and bibliometric analysis, invited experts to assess the variables by comparing the best and worst in terms of their significance to overall FMS performance. The outcomes of the BWM analysis not only offer insights into the factors affecting FMS performance but, more importantly, convey a nuanced ranking of these factors. The findings reveal a distinct hierarchy: the “Quality (Q)” factor emerges as the most critical, followed by “Productivity (P)” and “Flexibility (F)”. In terms of contributions, this study pioneers a novel and comprehensive approach to evaluating and ranking FMS performance variables. It bridges an evident research gap and contributes to the existing literature by offering practical insights that can guide manufacturing companies in identifying and prioritizing the most crucial performance variables for enhancing their FMS competitiveness. Our research acknowledges the potential introduction of biases through expert opinion, delineating the need for further exploration and comparative analyses in diverse industrial contexts. The outcomes of this study bear the potential for cross-industry applicability, laying the groundwork for future investigations in the domain of performance evaluation in manufacturing systems.