High-performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) is a powerful method for the microanalysis of compounds in biological samples. Compared with gas chromatography–mass spectrometry (GC–MS), this method is more broadly applicable to various compounds and usually does not require a derivatization step before analysis. However, when neutral sterols are analyzed, the sensitivities of usual HPLC–MS/MS method are not superior to those of GC–MS because the sterols are relatively resistant to ionization. In this review, we introduce the recent development of HPLC–MS/MS analysis for the quantification of non-cholesterol sterols. By adding an effective derivatization step to the conventional procedure, sterol analysis by HPLC–MS/MS surpassed that obtained by GC–MS in sensitivity. In addition, sufficient specificity of this method was achieved by selected reaction monitoring (SRM) and thorough chromatographic separation of each sterol.