A factory consists of numerous production workstations, multiple production lines and many production floors. Due to the characteristics of just-in-time and make-to-order mode manufacturing, small batches of production materials are required for production lines within a short period of time in order to facilitate daily production operations. In this paper, a real-time warehouse operation planning system (R-WOPS) for solving small batch replenishment problems is described. Through using R-WOPS, real-time production and warehouse operations are monitored by radio frequency identification (RFID) technology, and a genetic algorithm (GA) technique is applied to formulate feasible small batch replenishment solutions. Simulation tests show that R-WOPS generates pick-up and delivery route plans for small batch replenishment orders very efficiently.