Urinary metabolites and their concentrations serve as biomarkers for identification of metabolic pathways that relate to specific diseases; therefore, fast and accurate quantification of the metabolites in urine is essential in health assessment and diagnosis. As many urinary metabolites are of polar nature, hydrophilic interaction liquid chromatography (HILIC) has been used over the last several years because it offers faster and more reproducible analyses compared to traditional techniques such as reversed-phase chromatography or capillary electrophoresis. In our study, we developed a HILIC method by using a 3 cm analytical column in connection with tandem mass spectrometry detection for quantification of 10 urinary metabolites including creatinine as the reference for normalization. As all tested metabolites contain ionizable functional groups, pH of the mobile phase was optimized to achieve baseline separation of 2 isomeric pairs (1-methyl-4-imidazoleacetic acid/1-methyl-5-imidazoleacetic acid and 1-methylhistidine/3-methylhistidine) and to obtain overall better separation efficiency resulting in a 7 min analysis. The developed method was validated in terms of sensitivity, carry-over, linearity, matrix effects, accuracy, and precision. The metabolite concentrations in healthy subjects determined by the developed method correspond well with the normal reference values found in the literature. Moreover, the method was tested on a small cohort of COVID-19 patients, where it enabled identification of differences in metabolite levels. Thus, the developed method has potential to be used routinely in a diagnostic field for high-throughput analysis of urine samples.