Nowadays, advances in information and communication technologies, has provided an opportunity for banks to provide their electronic services to their customers in remote areas. This technological innovation by E–banking systems has brought about many benefits to customers while it has been accompanied by a number of risks including the operational ones. This risks need to be identified and managed by the Banks. The present research identifies, compares, and ranks factors affecting operational E-banking risks in viewpoints of customers and employees of Kermanshah Melli bank. To this end, a questionnaire was distributed to 300 employees and 384 customers of Kermanshah Melli bank by applying random cluster data collection method. The method of this study is descriptive- survey research. The study period covered the second half of the year of 2012. One-Sample T-Test, Friedman ranking Test and Independent Samples Test were employed to test hypotheses, to rank factors affecting operational risks and to compare the amount of effective factors on the operational risks of electronic banking among employees and customers Melli Bank respectively. The results indicate that hypotheses (1-5) support effects the factors (data accuracy, internal controls, technological infrastructure, access to systems, and security) have on Melli bank operational E-banking risks; hypothesis (6) ranks each of the 5-fold factors. In the security factors employees’ opinion is more effective than customers, but in factors (Data accuracy, Technological infrastructures) the trend is reversed. The study also includes recommendations in order to manage and lower operational E-banking risks.