Tyrosinase, trypsin, and tryptase are known to play important roles in melanin production of human skin. This paper describes the study of the inhibitory effect of Balanophora fungosa on melanin. The 50% EtOH extract obtained from B. fungosa indicated an inhibitory effect on mushroom tyrosinase activity with an IC(50) value of 15 μg/mL. Bioassay-guided fractionation of the active extract resulted in the isolation of four known compounds. Their structures were identified as 1-O-(E)-caffeoyl-3-O-galloyl-4,6-(S)-HHDP-β-d-glucopyranose (1), 1-O-(E)-caffeoyl-3,4,6-tri-O-galloyl-β-d-glucopyranose (2), caffeoyl-β-d-glucopyranose (3), and abietin (4) on the basis of spectroscopic analyses and comparison of their spectral data with those in the literature. Compounds 1 and 2 prevented pigmentation of melanin in a three-dimensional cultured human skin model. Furthermore, compounds 1 and 2 indicated inhibitory activities against trypsin and tryptase.