The long-chain polyunsaturated fatty acids (PUFA) found in fish oil, specifically eicosapentanoic acid (EPA) and docosahexanoic acid (DHA) play an important part in human health. As a result, fish oil supplements are commonly consumed by people around the world. Supplements in the form of triacylglycerols (TAG) can be sold at a premium price, compared to those in the ethyl ester (EE) forms. Producers of TAG supplements require a simple, rapid method to determine the authenticity of their raw material. Here, we describe a method to quantify EE in fish oil using solid phase microextraction headspace analysis and GCMS. Despite the variation in linear ranges of the calibration curves with volatility of the EE, 30 individual FA were quantified including common saturated FA such as palmitic and stearic acid, as well as longer chain PUFA, such as EPA and DHA. The method was then applied to three commercial fish oils in the TAG form and two of the products were found to contain EE, with one containing EE above 1.5% w/w, indicating that contamination had occurred. With growing consumer interest in fish oil products, the method proposed here will help resolve future issues of authenticity in fish oils.