A simple capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) method was developed for the analysis of free amino acids in commercial royal jelly (RJ) products containing various kinds of matrices. This method required no concentration step for sample preparation, and all 16 amino acids were determined without derivatization. The CE separation was achieved in an uncoated fused-silica capillary using a 1 M formic acid solution (pH 1.8) as the electrolyte, followed by MS/MS detection after mixing with a sheath liquid comprising 50% (v/v) methanol. The limits of detection (LODs) ranged from 0.61 to 10.5 μg (dry weight)/g for each amino acid. The recoveries for tablets, liquid drinks, and raw materials ranged from 88.3 to 108.6%, and the relative standard deviations (RSDs) were within 10%. The method was applied to 17 commercial RJ products, and the results were compared to those for honey. The relative proportions of free amino acids were specific for each RJ product, and the method was found to be useful in distinguishing not only among the different RJ products but also between RJ and honey.