The volatile fraction of unifloral Greek thyme honey was investigated by means of ultrasound-assisted extraction followed by GC-MS analysis. Phenolic compounds were the most abundant, followed by short chain fatty acids. In total, 14 compounds are proposed as potent botanical markers for thyme honey, 12 of which are phenolics. Among them, 3-hydroxy-4-phenyl-2-butanone and 3-hydroxy-1-phenyl-2-butanone were the most important, as their concentration averages more than 35 mg/kg of honey. Significant average proportions were found for 1-phenyl-2,3-butanedione, 3-hydroxy-4-phenyl-3-buten-2-one, 3,4,5-trimethoxybenzaldehyde and 3,4,5-trimethoxybenzoic acid. Minor phenolics with statistical significance (p < 0.0001) are phenylacetonitrile, vanillin, 4-hydroxyphenylethanol, 4-hydroxyphenylacetonitrile, and 2-hydroxyacetophenone. Phenylacetaldehyde, a common honey constituent is present at higher concentrations in thyme honey (p < 0.0001). Important non-phenolic components are 2-methylpropionic acid which was found at higher proportions in thyme honey (p = 0.002) and 4-(4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl)-3-buten-2-one, a norisoprenoid found solely in this type of honey.