The diffusion of water and oxygen molecules in the polybenzoxazine (PBO) matrix was studied at 295 and 450 K using fully atomistic molecular modeling. The hydrogen bonding of water and the hydroxyl groups in PBO is evident in the pair correlation function. The predicted diffusion coefficients for the two penetrants are remarkably close, although water forms hydrogen bonds with PBO but oxygen does not. The averaged hydrogen bond fraction and hydrogen bond lifetime were studied using the hydrogen-bonding autocorrelation function. The lifetime of the hydrogen bond between water and PBO is much shorter than the average residence time of the penetrant in a cavity, and therefore, the hydrogen bond does not remarkably retard the diffusion of water in the PBO matrix. The association of water is also observed.