System and method for load balancing multiple file transfer protocol (FTP) servers to service secure FTP sessions having encrypted signals are disclosed. In one aspect, embodiments of the system include multiple FTP servers coupled to a load balancing agent. Each of the multiple FTP servers is associated with a unique port range and the load balancer receives an encrypted data signal in a secure FTP session on a given port and uses a port range within which the given port falls to identify which of the multiple FTP servers a corresponding control signal of the secure FTP session was previously sent.