The article’s main goal is to describe the system design for the analysis of disinfection automated guided vehicle (AGV) utilisation so that the AGV’s optimal number can be determined. The simulation was used as the system’s main tool, allowing a relatively objective approach to imitate real system behaviour. With the proposed system, it is possible to determine the utilisation of AGVs and the number of necessary AGVs that carry out disinfection of the premises through the superstructure platforms. In the simulation model, two main modes of disinfection of ground AGV were tested. A regular circuit is carried out at specific intervals as well as a dynamic evaluation of the area and its possible contamination. When the area reaches a certain threshold, the instruction to disinfect the area is triggered. Experiments were carried out for a different number of AGVs, with the possible restriction of entry in the presence of the patient, and for a combination of specialised AGVs. Based on the results, we can conclude that the use of only surface-disinfecting AGVs is limited by the movement of patients and does not bring the same results as the use of a combination of surface- and air-disinfecting specialised AGVs.