In this paper we research positive and negative aspects of the application of e-business related with the introduction of e - invoice as the basic method of payment.  With the application of simulation tools IBM WebSphere Business Modeler, the simulation models of the existing payment processes (the classic invoice) and future e – model payment (e - invoice) were made. After having defined all the elements of these models with belonging costs per unit of time, the simulation study of the  invoice exchange between the private sector (Adriatic Security d.o.o.) and public sector (University of Zadar)  was  conducted. The aim of this simulation is the comparison of the existing model with the future electronic payment model. Limitations were observed related to the feasibility and justified introduction of the e - invoice for subjects who have relatively low annual volume of payment / invoice. Also, problems related to interoperability, security and archiving e – invoice are briefly discussed and proposed as important factors for future research.