This study examined the relationship between E-Payment System and Operational Performance of State-Owned Tertiary Institutions in Rivers State. Five objectives, five research questions and five hypotheses were formulated and tested. This study anchored on the positivist research paradigm; the study adopted the correlation survey research. The population of the study comprised of 21 managerial staff (Bursars, Registrars and Head of ICT units) of 6 tertiary institutions in Rivers State. Census was applied; the primary data source was adopted. A total of 21 managerial staff constituted the study subjects. The questionnaire was structured using the five-point likert scale. The Pearson Product Moment Correlation and Regression Model were employed to test the various hypotheses formulated for the study. From the analysis carried out, it was discovered that electronic payment system and ATM payment system showed a positive and significant relationship with operational performance of State-owned tertiary institutions in Rivers State. The study concluded that E-Payment System significantly relates with operational performance of State-owned tertiary institutions in Rivers State. Furthermore, the study recommends that state owned tertiary institutions in Rivers State should adopt e-wallet payment system as this would enable them serve students better and tertiary institutions in Rivers State should introduce ATM payment system in campuses in order to ease payment of school fees and other bills.