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Recently the passive optical network (PON) has attracted a lot of attention because it is an excellent solution for broad-band first mile services. Combining Ethernet frame with PON (EPON) and using synchronous optical code-division multiple-access (SOCDMA) technology are very promising for this application. In this paper, we analyze the jitter performance of SOCDMA-based EPON communication systems using perfect difference codes (PDC). We propose the joint jitter estimator and canceller (JJEC) to reduce the impact of jitter and multiple-user interference (MUI). The bit error rate (BER) of the system with JJEC is formulated analytically based on the correlator and the simple sampler receiver structures. The numerical results show that the proposed scheme can significantly suppress the MUI and improve the system performance.