The research paper Harmonization and standardization of information systems in the case of electronic banking payments in SEE in itself includes a current problem, because it deals with electronic payments that is every day becoming more current. The e-payment system includes the system of electronic instruments, procedures and infrastructure for transfer of money. It is important for all economic entities, since it is designed to allow quick and efficient execution of national and international payments. Central Bank is responsible for the National payment system, which manages accounts and bank depository of the institutions. In the Payment System of countries of SEE (South East Europe), Central bank has an operating function, and is responsible for development and oversight functioning of other payment systems in the country. In the following level are banks, that are responsible for the accounts of physical and legal persons. Each bank is decentralized to manage its customer accounts. This research deals with the comparisons of the management of electronic payments of different banks in Kosovo and other countries of SEE Region. The research in the paper is carried out to see and prove that economy and technology are becoming almost inseparable from one another. Electronic payments that are carried out in the financial institutions of the Republic of SEE, are managed in various ways, ranging from banks that have received great momentum in its implementation, to those institutions which do not exercise it at all. The research was conducted with several methods taking into account the method of comparison as the final approach to present achievements and conclusions. During the performing of research, we held interviews with some bank clerks, with the aim to realize and to explain System of electronic payments in the Country. The findings of the paper are that clients of banks in the Republic of Kosovo and other countries of SEE Region have just begun to realize the benefits of electronic payments, therefore this has reinvigorated their interest, to apply them. As we expected the results were positive, with the exception of some banks that do have more complicated procedures, so they have multiple levels of procedures for implementation of e-payment. The final conclusion of the paper consists on the fact that with solving of the problem of electronic payments,it will benefit both: customers, as well as financial institutions. DOI: 10.5901/ajis.2015.v4n2s1p112