The logistics of supplying agricultural products play a significant role in the development of the Ukrainian economy, which is a crucial link in the modernization of agriculture in the post-war era. Notably, the logistics of agricultural products face new risks and complex challenges in Ukraine. Therefore, it is necessary to define new models and design modern approaches to improving the logistics of supplying agricultural products. This upgrade contributes to the standardization and scaling of the Ukrainian agrarian product transportation system. The study presents the agrarian holding logistics system structure, operating in Ukraine, formed at two levels of interaction. The first level is the management and coordination system of an agricultural holding, the second is the relationship with the final elements of logistical interaction. The study proposed a conceptual framework as a modular interaction between the elements on three levels: fields of the agricultural holding, carrier using grain trucks transport, and grain elevators. This interaction process is described using Petri Nets. This mathematical tool is proposed for simulation model considering the stochasticity functioning between each link of supply chains. The simulation defines the delivery time for agricultural products from the agricultural holding. The model being proposed aims to facilitate decision-making in the management system of an agricultural holding. Its objective is to minimize the delivery time of value while accounting for changes in flow intensities, resource productivity, and work output volume, which follow certain distribution dependencies.