In modern high-speed military aircraft, the jet fuel has a secondary function acting as primary coolant to absorb the heat generated at high flight speeds and by on-board equipment. The present study deals with the development of a mathematical model for estimating the degradation of jet fuels in a simulated heated flow environment. Since many of the physical and chemical processes involved in the decomposition of real jet fuel in an aircraft are not well understood at this point, this model is formulated by taking an accurate description of the transport phenomena, but with a simplified global chemistry model. This model is also capable of utilizing the existing kinetic data information from batch reactors and predicting the jet fuel degradation in heated flow reactor systems. To develop and validate this mathematical model, however, it is necessary to have data from carefully instrumented experiments. The proposed model is validated using experimental data obtained at different flow rates after stressing a model jet fuel, dodecane. For the conditions examined, the model predictions agree well with the experimentally measured results. The numerical model also serves as a comprehensive simulation tool to examine the effects of various physical and experimental parameters on jet fuel degradation and evaluating additive effectiveness in flow reactors.