The physicochemical characteristics and flavor-related compounds of thigh meat derived from diverse Korean native chickens (KNC), namely Hanhyup No. 3 (HH3), Woorimatdag No 1 (WRMD 1), and Woorimatdag No 2 (WRMD 2), under fresh and frozen-thawed conditions were studied and compared with those of commercial broilers (CB). Regardless of the breed, KNC showed a higher (p < 0.05) percentage of linoleic and arachidonic acid. The highest proportion of docosahexaenoic acid was observed in WRMD 2. Despite having a higher collagen content, thigh meat derived from KNC maintained a similar texture profile in comparison to that of CB. The concentrations of most free amino acids (FAA), except for taurine, tryptophan, and carnosine, were higher in frozen-thawed meat than in fresh meat. Regarding volatile organic compounds (VOC), following freezing, the concentration of favorable VOCs increased in CB, but decreased in WRMD 1, suggesting a loss of pleasant flavor in frozen-thawed meat. This study indicated that changes in VOCs, including hydrocarbons (d-limonene, heptadecane, hexadecane, naphthalene, pentadecane, 3-methyl-, tridecane), esters (arsenous acid, tris(trimethylsilyl) ester, decanoic acid, ethyl ester, hexadecanoic acid, ethyl ester), alcohol (1-hexanol, 2-ethyl-), ketones (5,9-undecadien-2-one, 6,10-dimethyl-), and aldehydes (pentadecanal-, tetradecanal, tridecanal), may be a promising marker for distinguishing between fresh and frozen-thawed chicken thigh meat. These findings are of critical importance as preliminary data for developing high-quality chicken meat products.