Urinary biopterin (Bio) and neopterin (Neo) are important markers for clinical diagnosis of hyperphenylalaninemia. Herein, we developed a high-throughput analysis method based on electrospray ionization mass spectrometry (ESI-MS) with polymer tips for the rapid quantitative detection of Bio and Neo in clinical urine samples. Different polymer tips were investigated. It is found that the best detection sensitivity was achieved with hydrophobic polymer tip, ie, polyethylene tips. The high-throughput polymer tip-ESI-MS method allowed a rapid analysis speed at ~40seconds per sample. The limits of quantification (LOQ) (S/N≥10) for the detection of Bio and Neo were improved to be 5.0ng/mL. Acceptable relative standard deviation (RSD) values for Neo and Bio were measured to be 12.2% and 13.4% for direct measurement of Bio and Neo in raw urine samples, respectively. Furthermore, Bio and Neo were directly quantified from 18 clinical urine samples by presented method. The ratios of urinary Bio-to-Neo were analyzed for diagnosis of hyperphenylalaninemia. The results demonstrated that the present polymer tip-ESI-MS method is a promising strategy for the rapid analysis of clinical samples.