An algorithm for stochastic perturbation of the semi-Lagrangian trajectories is implemented in the ensemble weather prediction system based on the global atmosphere model SL-AV20 with a horizontal resolution of approximately 20 km, 51 vertical levels, and Local Ensemble Transform Kalman Filter (LETKF). The combined use of methods for stochastic perturbation of trajectories and the parameters and tendencies of subgrid-scale processes parameterizations allows to generate ensembles with a larger spread compared to ensembles without stochastic perturbations of trajectories. An improvement in probabilistic estimates of the ensemble forecasts for various variables is shown. The comparison of two versions of ensemble prediction system is presented.