Increasing popularity of online banking systems instead of traditional branch networking requires understanding customer behaviors as users of such systems. This research aims to investigate online banking acceptance among Bosnian university students by considering system, user, acceptance and performance related factors by considering a new relationship between perceived system security and perceived system quality. According to the results, the users perceive that (1) online banking system is not secure and poorly qualified but useful and easy to use; (2) the users themselves are slightly capable of using the system; (3) they have intention to use the system but don’t use the system; and (4) they are slightly satisfied with the system and increase their benefits. The results also provide that all hypotheses except the relationship between perceived ease of use and intention to use are supported. Perceived System Security, as a new dimension, is found to have positive effect on Perceived System Quality. It can be implied that if the system is qualified and the users are self-efficient about using the system, they perceive the system as easy to use and useful. It is suggested that banks better take necessary steps to persuade their customers about the system security and usefulness in completing their tasks.