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Black garlic is currently attracting interest as a health food and constituent of commercial supplements; however, no data regarding the <span style="font-variant: small-caps;">d</span>-amino acids within black garlic have been reported. Therefore, the amino acid compositions of methanol extracts from fresh and black garlic were compared herein. We investigated the contents of the <span style="font-variant: small-caps;">d</span>- and <span style="font-variant: small-caps;">l</span>-forms of amino acids in commercial fresh, black, and freeze-dried garlic foodstuffs by liquid chromatography–tandem mass spectrometry (LC–MS/MS) using a pre-column chiral derivatization reagent, succinimidyl 2-(3-((benzyloxy)carbonyl)-1-methyl-5-oxoimidazolidin-4-yl) acetate. Several <span style="font-variant: small-caps;">d</span>-amino acids, namely, the <span style="font-variant: small-caps;">d</span>-forms of Asn, Ala, Ser, Thr, Glu, Asp, Pro, Arg, Phe, Orn, Lys, and Tyr, were observed in the methanol extract of black garlic, whereas only <span style="font-variant: small-caps;">d</span>-Ala was detected in that of fresh garlic foodstuffs. These data suggest that several <span style="font-variant: small-caps;">d</span>-amino acids can be produced during fermentation for preparing black garlic.