This paper presents an analysis of cycle times and throughput performances of Shuttle-Based Storage and Retrieval Systems (SBS/RSs), a relatively new technology that is becoming an important part of automated warehouses. A parametric simulation model was developed for the purposes of this research. The model enables calculation of Single Command (SC) and Dual Command (DC) cycle times and throughput performances of SBS/RS. The model was tested on a case study, which is based on a real type of SBS/RS. Experiments were designed to evaluate the following factors, such as number of bays n x and minimum warehouse volume Q. Our research uses Design of Experiment (DOE) analysis and helps to achieve the proper dimension of the SBS/RS, which gives us the best possible performance of the SBS/RS. The simulation based on the presented model delivers the best SBS/RS designs.