Promising developments and further improvements of cyber physical logistics systems (CPLS) and automated guided vehicles (AGV) lead to broader application of such systems in production environments and smart factories. In this study a new mixed integer linear program (MILP) is presented for the scheduling of AGVs in a flexible reentrant job shop with blocking. Optimal solutions to small instances of the complex scheduling problem in a make-to-order production, minimizing the make span, are calculated. Different numbers of jobs are considered. Feasible schedules for the machines and the AGVs are generated from different sized instances to evaluate the limits of the mathematical model.