Previous research has clearly and consistently shown that flow time advantages accrue from splitting production lots into smaller transfer batches or sub-lots. Less extensively discussed, and certainly undesired, is the fact that lot splitting may dramatically increase the number of setups required, making it impractical in some settings. This paper describes and demonstrates a primary cause of these “extra” setups. It then proposes and evaluates decision rules which selectively invoke lot splitting in an attempt to avoid extra setups. For the closed job shop environment tested, our results indicate that conditional logic can achieve a substantial portion of lot splitting’s flow time improvement while avoiding the vast majority of the additional setups which would be caused by previously tested lot splitting schemes.