Security is a critical issue of the modern file and storage systems, it is imperative to protect the stored data from unauthorized access. We have developed a file security system named as Java File Security System (JFSS) [1] that guarantee the security to files on the demand of all users. It has been developed on Java platform. Java has been used as programming language in order to provide portability, but it enforces some performance limitations. It is developed in FUSE (File System in User space) [3]. Many efforts have been done over the years for developing file systems in user space (FUSE). All have their own merits and demerits. In this paper we have evaluated the performance of Java File Security System (JFSS). Over and over again, the increased security comes at the expense of user convenience, performance or compatibility with other systems. JFSS system performance evaluations show that encryption overheads are modest as compared to security.