The paper concerns a development of an approach for implementing fault-tolerant control (FTC) of automated guided vehicles (AGVs). The main challenge considered in the article is the way of taking into account in the scheduling algorithm the delays occurring in the system resulting from the use of transport means. Mostly, multiple AGVs are designed and implemented as a firm real-time system in which delays are treated as faults. The proposed framework allows to compensate the faults in the real time. In the paper a multiple AGVs that transport item from an output of a production system to a high bay warehouse is presented. The article presents the non-deterministic nature of a multi-AGV system and includes a mathematical description of the system using (max, +) algebra. Having a analytical description of AGVs system, a new FTC strategy is proposed. Moreover, in the paper an illustrative case study showing the performance of the developed approach is presented.