The body of literature on the impact of emulsion particle size on oxidation rates is unclear. This could be because emulsions are typically polydisperse and the oxidation rate of individual droplets is impossible to discern. Flow cytometry is a technique for studying individual cells and their subpopulations using fluorescence technologies. It is possible that individual emulsion droplets could also be characterized by flow cytometry as a novel approach for studying lipid oxidation. Typical emulsion droplets are too small to be visualized by flow cytometer, so emulsions were prepared to have droplets > 2 μm; weighting agent and xanthan gum were added to minimize creaming during storage. A radical-sensitive lipid-soluble fluorescence probe (BODIPY665/676) was added to the lipid used to prepare the emulsion so that the susceptibility of individual emulsion droplets could be determined. The results showed that in a polydisperse emulsion system, small droplets were oxidized faster than large droplets. Using mixtures of emulsions with and without prooxidants, it was possible to see the transfer of prooxidants between droplets, a process that is influenced by surfactant and salt concentrations. For example, surfactants micelles can transfer prooxidants to neighboring non-oxidized droplets and cause fluorescence loss when surfactant concentration was higher than critical micelle concentration (CMC). Transfer of prooxidants was promoted by adding NaCl and free fatty acid which could be attributed to the lower CMC. This study showed the potential for applying flow cytometry on oxidation of individual emulsion droplets.