Positron emission tomography (PET) is a practical tool for range verification of hadron therapy. As well, the quantitative washout of the positron emitters has a potential usefulness as a diagnostic index, but the modelling for this has not been established. In this study, we measured washout rates of rabbit brain and performed kinetic analysis to explore the washout mechanism. Six rabbit brains were irradiated by 11C and 15O ion beams, and dynamic PET scan was performed using our original depth of interest (DOI)-PET prototype. The washout rate was obtained based on the two-compartment model, where efflux from tissue to blood (k2), influx (k3) and efflux (k4) from the first to second compartments in tissue were evaluated. The observed k2, k3 and k4 of 11C were 0.086, 0.137 and 0.007 min−1, and those of 15O were 0.502, 0.360 and 0.007 min−1, respectively. It was suggested permeability of a molecule containing 11C atoms might be regulated by a transporter. The k2 of 15O was comparable with 15O-water. This study provides basic data for modelling of the washout effect.