A simultaneous quantitative profiling method for androgens and prostaglandins using ultra-high-performance liquid chromatography-tandem mass spectrometry was developed and validated to evaluate urinary androgen and prostaglandin levels. Solid-phase extraction and liquid-liquid extraction steps were combined during the sample preparation. β-Glucuronidase/arylsulfatase was also used in the enzyme hydrolysis step. Chemical derivatization was performed using 2-hydrazinopyridine for simultaneous determination of androgen and prostaglandin in the same ionization mode. The analytes were all separated and measured using multiple reaction monitoring in the positive ion mode within a run time of 22 min. The method was validated, achieving overall recoveries ranging from 81.0 to 102.9% with limits of quantification ranging from 0.01 to 2 ng/mL. The intra-day accuracy and precision ranged from 6.5 to 14.3% and from 77.1 to 106.8%, respectively. The inter-day accuracy and precision ranged from 8.9 to 18.2% and 89.9 to 101.4%, respectively. The linearity was expressed using the correlation coefficient, which was >0.99. The method developed herein was used to investigate the effects of a one-year finasteride treatment through differences in urinary androgen and prostaglandin levels between treated male pattern baldness patients and normal controls. The urinary androgen and prostaglandin levels were not significantly different between the two groups because of the administration of finasteride. The results confirmed that finasteride affects androgens and PGs related to hair regrowth and growth length, and a one-year finasteride treatment is effective for MPB. The mass spectrometry-based quantitative profiling method used herein for the investigation of male pattern baldness also holds great potential for the evaluation of androgens and prostaglandins associated with the metabolism of various inflammatory diseases.