Electronic payment system in one of the e-banking services and must be reliable and free of security deficiencies in order to overcome traditional system. Improving customer’s perceptions of security and trust in the course of electronic payment transactions is vital in order to attract, retain and retrieve users of such a system. This study aimed to investigate the effects of customers’ perceptions of security and trust on their use of the Agriculture Bank of Iran’s e-payment system. Correlation-type descriptive research was used as a research method and hypotheses were tested by structural equations model. Results of conceptual framework hypotheses’ test showed that transaction processes and technical security variables have positive and significant effects on perceived security, transaction processes and security statement variables relate positively and significantly with perceived trust, perceived trust affects extent of use positively and perceived security have significant and positive relationship with perceived trust.