Supercritical fluid chromatography (SFC) owes many of its advantages to the properties of supercritical CO2, which possesses benefits as mobile phase. SFC has recently gained attention as a separation technique because it can be utilized for not only non-polar but also polar compound analysis. In addition, MS is widely adopted for SFC, and the options for MS are equivalent to liquid chromatography. Sensitive and selective detection is crucial in metabolite analysis. The SFC/MS system can be an alternative approach to liquid chromatography, as can metabolite analysis using packed-column SFC in biosamples. In this review we cover the fundamentals of SFC in combination with MS, and discuss the results of metabolite analysis using SFC/MS.