For quick and effective response to dynamically varying market demands, it is strongly required to make flexible manufacturing systems more efficient by introducing effective and autonomous control and management system. For efficient operation, it is important to decide which work in which area, such as warehouse, loading station, buffer and machining centers in the FMS to be transported to which area. This paper deals with an FMS with RGV for small products in which more than one small works are loaded on one pallet for processing and proposes an auction-based scheduling method for the FMS which is applied to select and assign a work to RGV. The characteristics and effectiveness of the proposed method are discussed in comparison to the one for the FMS processing large products.