Hybrid manufacturing systems (HMSs) are attracting attention from academia and industry owing to concerns regarding fluctuations in customers' demands. An HMS combines traditional manufacturing cells and a functional area, leading to improved flexibility in meeting customers' demands Although information on HMSs is available in the existing academic literature, scheduling problems with walking workers for such systems are rarely addressed. This study explores a multi-objective scheduling problem in HMS and proposes an optimization model to achieve three objectives (i) minimization of average flow time, (ii) reducing the maximum number of workers, and (iii) minimization of the maximum number of workers changing. The model belongs to a non-deterministic polynomial-time hardness (NP-hard) problem class, and hence, non-dominated sorting algorithm-II (NSGA-II) with a local search procedure is employed. The proposed algorithm and several widely accepted multi-objective evolutionary algorithms are compared for six different cases. A set of evaluation metrics is used to evaluate the effectiveness of the proposed algorithm in finding desirable solutions. The computational results indicate that the proposed algorithm is superior to other metaheuristics. This study contributes to existing academic literature by investigating lot scheduling problem with walking workers in the context of hybrid manufacturing systems and provides guidelines for researchers and industry practitioners.