The aim of this paper is to study and compare two different scheduling rules for operations of transactions in shuttle-based storage and retrieval system (SBS/RS) to observe how scheduling rule affects the system performance. SBS/RS is one of the emerging automated warehousing technologies mostly utilized by large distribution centers due to its advantages of fast transaction process rate. Although the increased transaction rate is because of the system (warehouse) design of having multiple numbers of autonomous shuttles in the system, operational rules such as scheduling of waiting transactions in queues may also play a significant role in increasing the system performance. For this purpose, we implement first-in-first-out (FIFO) and shortest processes (i.e., travel) time scheduling rules for selecting waiting transactions in shuttle queues to investigate how these rules affect the performance of the system. We simulate the system under different racking designs and arrival rate scenarios and observe the system performance metrics in terms of average cycle time (e.g., throughput rate) and average energy consumption per transaction, separately. The results suggest that the SPT scheduling rule outperforms FIFO rule, especially for the throughput rate performance metric.