To provide an automated warehouse system capable of efficiently handling vacant pallets without forcing to sacrifice a cargo handling area.

The automated warehouse system 4 comprises a housing shelf 11 forming a plurality of housing blocks 22 for housing bagged objects W placed on pallets P, a transfer means 12 for carrying in and out the objects W with the pallets P between the housing shelf 11 and an entrance/exit 4a for carrying in nad out the objects, and a control device for controlling carrying in and out the objects with the pallets P. The transfer means 12 is provided with a warehoused pallet stacking function for stacking the warehoused vacant pallets P on the housing shelf 11.