Tomato fruit act as a model fruit to study climacteric ripening. Since ethylene (C2H4) biosynthesis is an important final step in the process, O2 may play a key role in tomato ripening. We developed a reaction-diffusion model to predict the O2 distribution within a tomato fruit based on a 3-dimensional geometric fruit model distinguishing different tissues (mesocarp, septa, placenta, columella, gel and seeds) obtained by magnetic resonance imaging (MRI). Coefficients of specific effective O2 diffusion, we obtained from X-ray micro-computed tomography (μ-CT) based pore network models, and tissue-specific respiration rates were measured from depletion experiments. The results revealed hypoxia in the gel part of a ripe tomato as a result of the diffusion resistance and respiration of the gel and seeds. Relatively high O2 concentrations were seen in the central and outer pericarp tissues, due to O2 supply through the pedicel scar and the high diffusivity of the porous tissues. Excellent agreement was found between the predicted oxygen profiles in the fruit and those measured using a micro electrode O2 sensor. This model will be further extended to include the generation and distribution of C2H4 in tomatoes to explore whether O2 is the key factor in sequential ripening within tomatoes.