We present a hybrid configuration of joint transform correlator (JTC) and joint fractional transform correlator (JFTC) for encryption purpose. The original input is encoded in the joint fractional power spectrum distribution of JFTC. In our experimental arrangement, an additional random phase mask (master key) is holographically generated beforehand by a Mach–Zehnder interferometer with a JTC as the object arm. The fractional order of JFTC, together with the master key, can remarkably strengthen the safety level of encryption. Different from many previous digital-holography-based encryption schemes, the stability and alignment requirement for our system is not high, since the interferometric operation is only performed in the generation procedure of the master key. The advantages and feasibility of the proposed scheme have been verified by the experimental results. By combining with a multiplex technique, an application for multiple images encryption using the system is also given a detailed description.