In this paper, we propose a periodic control strategy for the assignment of the tasks to several AGVs (Automated Guided Vehicles) in dynamic transportation. In the proposed method, all of the transportation tasks that arrive at a time are collected during a given time period and an efficient scheme of the assignment is generated by the optimization procedure, that has to be completely executed during the next period. An meta-heuristic algorithm called pheromone communication method is adopted as an optimization method for minimizing the traveling time of AGVs while maintaining a short computation time. In our study, the optimal number of collecting new tasks is investigated by changing the various timing of sending the requests to AGVs in the numerical experiments. The effectiveness of the proposed method is demonstrated by comparing the total throughput of an AGV system with that of the conventional method for a large scale transportation bay.