Technology development, particularly Tele-communication and informa-tion technology developments have changed Banking industry. Many studies and researches have explained E-banking developments and its operations. Also, a lot of researches have been conducted on E-banking and factors affecting on it, but there is a few/no research about E-banking challenges. This research wants investigate the E-banking challenges from Banking system's customers and managers, and use fuzzy AHP in order to rank the E-banking challenges. The results of this research shows that from Banking system's managers perspective, the most important of E-banking challenges are: customer's information privacy, internet security, and customer's trust; while from customer's perspective, the most important of E-banking challenges are: Bank's reputation, availability of online banking legal regulations, provide more reliable, faster, easier and diverse service. Although, the results of this research show that there is not agreement between Banking system's managers and customers, apparently; but it can argued that the reputation of a bank is contingent to provide more reliable, faster, easier, diverse service, and also keep customer's information privacy.