The process of photo-degradation, during photodynamic therapy, has important implications for both the diagnostic and therapeutic potential of specific photosensitizers. Monitoring photo-degradation may provide a useful indicator of the local concentration of singlet oxygen, and therefore a direct measure of photodynamic effectiveness. The spectroscopic properties of protoporphyrin IX (PpIX), the photosensitizer generated by the precursor 5-aminolevulinic acid, have been well documented. By recording the fluorescence emission spectrum of PpIX during illumination (at 630 nm) the photo-degradation of the sensitizer can be recorded. The rate of PpIX photo-degradation is dependent on the concentrations of both the sensitizer and molecular oxygen, but the decay cannot be described by a simple function that is valid under a variety of experimental conditions. By numerically solving differential equations describing the instantaneous concentrations of species in the photo-oxidation pathway of PpIX, we have been able to model the dynamics of sensitizer fluorescence under varying conditions of sensitizer concentration, oxygen concentration and illumination irradiance. Results are consistent with those measured in aqueous solution.