For years, there have been tremendous endeavors to reduce makespan in an attempt to decrease the production expenses. This investigation aims to develop a scenario-based robust optimization approach for a real-world flow shop with any number of batch processing machines. The study assumes there are some uncertainties associated with processing times as well as size of jobs. Each machine can process multiple jobs simultaneously as long as the machines’ capacities are not violated. In order to verify this developed model and to evaluate the performance of the proposed robust model, a number of test problems are prepared and a commercial optimization solver is adopted to solve these test problems. For the purpose of validating the results, the robust model and mean-value model are carried out by simulation, which confirmed the proposed model.