The current prostate cancer (PCa) diagnosis, based on the blood prostate-specific antigen (PSA) level measurement, is not a precise science. The widely used PSA biomarker for PCa has poor sensitivity and specificity and often leads to false-negative and false-positive test results. Recently, sarcosine, proline, kynurenine, uracil, and glycerol 3-phosphate were found in higher concentrations in metastatic prostate cancer urine samples. By measuring all five of these metabolites, doctors may be better able to diagnose prostate cancer with high accuracy. However, there is no method reported for simultaneous detection of these compounds in urine samples. In this study, a novel method was developed to separate and quantify six urinary metabolites including creatinine in urine samples by using liquid chromatography/tandem mass spectrometry. Chromatographic separations of the analytes were carried out using a phenyl-hexyl column with 0.1% formic acid in water and acetonitrile, respectively, under a gradient program. The six metabolites were detected in the multiple reaction monitoring modes with the ESI-positive mode. The linear range of the analytes was from 0.003 to 40 µmol/L. The limit of detection was from 0.05 to 4 nmol/L, and the limit of quantification ranged from 3 to 20 nmol/L. The factors affecting the separation and quantification of the six metabolites, such as mobile-phase and MS conditions, were also investigated. The technique developed in this study is simple, fast, sensitive, and selective. It can be used for quantifying these six metabolites in urine samples for potential early cancer screening.