The model for simulating the influence of intensity scintillation on pulse arrival time jitter is established based on the principle of multiple phase screens and the power spectral inversion method. The pulse arrival time jitter is simulated under different receiving apertures and different transmission distances. The simulation results show that the pulse arrival time jitter shows a positively skewed distribution under the condition of aperture receiving. A large receiving aperture can effectively suppress the pulse arrival time jitter. The variation of transmission distance has less influence on the pulse arrival time jitter at the far end compared with at the near end. An experimental platform for the pulse arrival time jitter caused by atmospheric turbulence is established, the second pulse waveform propagating through a turbulence channel is collected, and the pulse arrival time is determined by threshold detection. The experimental results show that the distribution of pulse arrival time jitter is consistent with the theoretical analysis results.