Molecular dynamics (MD) simulations were employed to estimate the diffusion coefficients of small gas molecules (Ar, O2, N2, CO2, and CH4) in amorphous cis-1,4-polybutadiene in the temperature range of 250–400K. The VT diagram and solubility parameter of the amorphous polymer have been successfully reproduced using a full atomistic potential. Diffusion coefficients were calculated from long NPT MD runs (up to 3ns) at temperature ranging from 250 up to 400K. Calculated diffusion coefficients compare well with experimental data as well as previous published work, though a systematic overestimation is found due to the finite-size effect of the model. The influence of various physical and computational parameters on the results is discussed. The diffusion mechanism is examined at the different temperatures of study.