A polarization diversity-based PON system can be an attractive network solution for the future PON system that requires high data capacity with both a large number of subscribers and longer transmission-reach. However, the state-of-polarization (SOP) inevitably rotates during the transmission through the single-mode fiber (SMF). Therefore, this system cannot ensure high data capacity owing to the SOP rotation. In this paper, we propose the out-of-band pilot-aided SOP rotation tracking technique for in the polarization diversity-based PON transmission system. The proposed technique tracks the SOP rotation by measuring the variance of the power ratio of the inserted pilot-tone at the reference polarization axis. This technique offers the advantages of a low overhead and dynamic update for SOP variation; further, it is optical control-free and transparent for data format. For the experimental demonstration of the SOP rotation compensation, the pilot insertion was firstly optimized and the correctable range of the SOP rotation was analyzed. The results of the emulation of the uplink transmission indicated that the SNR at both polarization axes could be successfully retained by compensating the SOP rotation. Under the target forward error correction limit, the SE up to 8 bit/s/Hz within single-wavelength was obtained for 60 km PON transmission.