Phytochemical investigation on the polar constituents in the aerial parts of Thymus quinquecostatus var. japonica resulted in the isolation of three flavonoids along with four known phenolic components. The isolated compounds were characterized as 2(S)-5,7,3′,5′-tetrahydroxyflavanone (1), (+)-taxifolin (2), (+)-aromadendrin (3), rosmarinic acid (4), caffeic acid (5), protocatechuic acid (6), and protocatechuic aldehyde (7) from comparisons of their physicochemical and spectroscopic data 1H-, 13C-NMR, two-dimentioal NMR, and mass spectrometery) with those of authentic samples and reference data. This is the first report on the isolation of compounds 1–7 from T. quinquecostatus var. japonica. In addition, compounds 2 and 4 exhibited the most potent pancreatic lipase inhibitory activities in a concentration-dependent manner with IC50 values of 15.4±0.8 and 62.8±2.7 μM, respectively.