Significant funds have been allocated to maintain road networks each year in developed countries. Performance prediction is crucial for pavement management systems to adjust working plans and budget allocation. As a Bayesian nonparametric method, Gaussian process regression (GPR) is powerful in predicting nonlinear time series and quantifying uncertainty. However, it remains computationally intensive and fails to adapt to the time-varying characteristics. To address such issues, a dynamic GPR model is proposed for probabilistic prediction of the International Roughness Index (IRI) for flexible pavements. A moving window strategy is developed to substantially shrink the size of training data, which effectively alleviates computational cost and thus leads to a dynamic GPR. A genetic algorithm is then adopted to determine the optimal window size by considering the trade-off between computational efficiency and accuracy. A dataset acquired from Long-Term Pavement Performance (LTPP) is used to demonstrate the feasibility of the dynamic GPR. Its performance is compared to traditional GPR as well as dynamic and static Bayesian linear regression (BLR) models. The comparison results indicate that the proposed dynamic GPR can increase the accuracy by 0.86, 1.52, and 2.27 times for dynamic BLR, static GPR, and static BLR, respectively. It exhibits the best results in terms of accuracy and uncertainty metrics due to its nonlinear modelling and time-varying ability.