A low-cost flow system was designed, manufactured, and tested to perform automated base-catalyzed transesterification of triacylglycerols to determine the fatty acid content in edible oils. In combination with traditional gas chromatographic analysis (GC-FID), this approach provides a semi-automated process that requires minimal manual intervention. The main flow system components, namely syringe pumps, connectors (i.e., flangeless fittings), and reactors, were manufactured using 3D-printing technology, specifically fused deposition modeling (FDM). By fine-tuning 3D-printer settings, high-quality leak-tight fittings with standard threading were manufactured in polypropylene (PP), which reduced the overall cost of the flow system significantly. Due to the enhanced reactivity in flow, lower catalyst concentrations (≤ 1.5 wt.%) were needed compared to traditional batch reactions (5 wt.%). The suitability of the automated flow method was determined by comparing results with the certified fatty acid content in sunflower seed oil from Helianthus annuus. Acceptable levels of accuracy (relative errors < 5%) and precision (RSD values ≤ 0.02%) were achieved. The mostly 3D-printed flow system was successfully used to determine the fatty acid content of sunflower and other commercial edible oils, namely avocado oil, canola oil, extra virgin olive oil, and a canola and olive oil blend. Linoleic acid (C18:2) was the major component in sunflower oil, whereas all other oils consisted mainly of oleic acid (C18:1). The fatty acid content of the edible oils was comparable to certified and literature values.