The article presents the methodology of the logistic system simulation in the Petri Nets environment on the example of agro-products delivery from Ukraine to the Netherlands, as well as a set of case-studies that can be used as didactic means for course "The modeling of transport processes" to teach the future transport industry specialists. The content, features and capabilities of the Petri Nets in the logistics systems simulation have been analyzed. A structural logistic system model of agro-products delivery, which takes into account the operation sequence, the combination peculiarities and the use resources in each subsystem, has been constructed in the Petri Nets. A time criterion has been proposed to determine the effective option for agro-products delivery. According to the results of the logistics system simulation in the Petri Nets environment, a statistical analysis of the parameters has been carried out. It has been made a choice of a suitable option of the delivery scheme allowing for the time spent and the magnitude of the possible costs associated with the use of certain transport modes. It has been made conclusion about feasibility of creating the case-study set, which is based on real facts and being solved in the Petri Nets environment, in order to organize the future transport industry specialists' study and research activities.