Changes in atmospheric oxygen concentration over Earth history are commonly related to the evolution of animals and plants. But there is no direct geochemical proxy for O2 levels, meaning that estimations rely heavily on modeling approaches. The results of such studies differ greatly, to the extent that today’s atmospheric mixing ratio of 21% might be either the highest or lowest level during the past 200 m.y. Long term oxygen sources, such as the burial in sediments of reduced carbon and sulfur species, are calculated in models by representation of nutrient cycling and estimation of productivity, or by isotope mass balance (IMB)—a technique in which burial rates are inferred in order to match known isotope records. Studies utilizing these different techniques produce conflicting estimates for paleoatmospheric O2, with nutrient-weathering models estimating concentrations close to, or above, that of the present day, and IMB models estimating low O2, especially during the Mesozoic. Here we reassess the IMB technique using the COPSE biogeochemical model. IMB modelling is confirmed to be highly sensitive to assumed carbonate δ13C, and when this input is defined following recent compilations, predicted O2 is significantly higher and in reasonable agreement with that of non-IMB techniques. We conclude that there is no model-based support for low atmospheric oxygen concentrations during the past 200 m.y. High Mesozoic O2 is consistent with wildfire records and the development of plant fire adaptions, but links between O2 and mammal evolution appear more tenuous.