The purpose of this paper is to look at the Constraints of Implementing an E-Banking Security System Configuration at Rural Banks in North Sumatra, Indonesia. This type of research is qualitative research, namely research that intends to understand the phenomena experienced by the research subjects such as behavior, perceptions, motivations, actions, etc. holistically, and by means of descriptions in the form of words and language, in a special context that naturally and by utilizing various natural methods. The results of this study conclude that the obstacles in the implementation of the E-Banking security system in BPR, in the form of preventive measures and also risk analysis on the implementation of the E-Banking security system application in BPR.