Low security and high peak-to-average power ratio (PAPR) are two major challenges for orthogonal frequency division multiplexing passive optical network (OFDM-PON) systems. This study proposes a secure selective mapping (SLM) scheme based on two-dimensional chaotic encryption. The subcarriers of OFDM signals are scrambled by the random interleavers and phase sequences generated using a two-dimensional logistic map to achieve both encryption and PAPR reduction. The simulation results show that compared with the conventional SLM and original optical OFDM (O-OFDM) signals, the proposed scheme can obtain PAPR suppression gains of 0.5 dB and 3.8 dB, respectively. The experimental results demonstrate that a 7 Gbit/s 16-quadrature-amplitude-modulation (16QAM) O-OFDM encrypted signal can be securely transmitted in the intensity modulation/direct detection OFDM-PON system through a 25-km standard single-mode fiber. Moreover, the bit error rate performance of OFDM-PON systems is considerably improved.