An ordinary Petri‐net (PN) based approach is proposed to design the programmable logical controller (PLC) for preventing collisions between vehicles in an automated guided vehicles (AGV) system. First, method is proposed to model an AGV system as an ordinary PN, called the plant PN. Second, for collision prevention in an AGV system, module control methods are proposed to design the PN supervisor (the closed‐loop PN) by augmenting the plant PN. In detail, three modules are defined the line, divide, and merge modules, in the plant PN, and the control module methods are presented for each of these three modules. As a result, the closed‐loop PN of an AGV system is obtained and can be analyzed using the PN theory. Finally, method is proposed to translate a closed‐loop PN into a ladder diagram. Consequently, the PN supervisor is implemented by a PLC using these proposed methods. A laboratory AGV system is used to illustrate this approach.