A non-aqueous flow injection method for determining free fatty acid (FFA) content in corn and sunflower oil samples was developed. A single-line manifold system was built by modification of an HPLC for flow injection analysis (FIA). Without pre-treatment, oil samples were injected into a n-propanol solution containing KOH and phenolphthalein (PHP). The main parameters, such as flow rate of carrier phase, length, geometry, inner diameters of the coils and reagent concentration were all optimized. The proposed FIA method was validated for precision, accuracy, linear region, limit of detection (LOD) and limit of quantification (LOQ). The intra- and inter-day measurements of the precision of the method were found to be within the limits of acceptance criteria (RSD < 1%), and were rugged when the method was performed by a different analyst. The linear concentration range was calculated as 0.09-1.50 and 0.07-1.40 FFA% for corn and sunflower oils, correspondingly. The LOD and LOQ were found to be 7.53 × 10(-4)-2.28 × 10(-3) oleic acid % and 7.11 × 10(-4)-2.23 × 10(-3) oleic acid % for corn and sunflower oils, respectively. The results were compared with those obtained by the AOCS (Ca-5a-40) method using statistical t and F tests, and a significant difference was not observed between the methods at a 95% confidence level. The proposed method is suitable for quality control of routine applications due to its simplicity, high sample throughput, and economy of solvents and sample, offering considerable promise as a low cost analytical system that needs minimum human intervention over long periods of time.