A method based on direct protein precipitation-ultra performance liquid chromatography was established for the determination of trace 5-fluorouracil in serum. The samples were pretreated with 6% perchloric acid as the precipitant and 5-chlorouracil as the internal standard, and the supernatant separated after vortex mixing and high speed centrifugation was used as the test sample. The separation was carried out with an Acquity HSS T3 column and the mobile phase consisting of water and acetonitrile, and the flow rate was 0. 2 mL/min; the injection volume was 5 μL, and the column temperature was 20 °C. The key parameters of this method such as specificity, accuracy, precision and linearity, were validated. Compared with other methods, this method can complete the analysis with significantly reduced time and cost. The established method is useful for therapeutic drug monitoring of 5-fluorouracil plasma concentration and it has been successfully applied in clinical cases.