Owing to its favorable properties, such as low viscosity and high diffusivity, a supercritical fluid can be used as the mobile phase in chromatography. Supercritical fluid chromatography (SFC) can provide high-speed and high-resolution separation. Since supercritical carbon dioxide (SCCO(2)), which is generally used as the mobile phase in SFC, is automatically emitted at room temperature, SFC is most commonly used as a preparative method. However, SFC can also be used to perform high-precision biomolecular analysis, especially for hydrophobic metabolites, because of the low polarity of SCCO(2). The use of a mass spectrometer with SFC can widen the scope of application of SFC to bioanalysis. In this review, we summarize practical application of SFC as a tool for the analysis of metabolites in real biological samples.