The aim of this study was to evaluate the inhibitory activity of compounds isolated from the aerial parts of Hedyotis pilulifera (Pit.) T.N.Ninh toward selected cancer cell lines. The isolated compounds were identified by analyzing their nuclear magnetic resonance spectral data and physical properties, and comparison of these with reported data. The sulforhodamine B assay was used for the cytotoxic evaluation of isolates. Among twenty-one compounds isolated from H. pilulifera, compounds 2, 3, and 4 showed moderate inhibitory effect on MCF-7 with IC 50 values of 63.5, 59.4, and 52.7 µg/mL, respectively, while the other compounds exhibited no effect (IC 50 values > 100 µg/mL). Further investigation using HT29, LU-1, HL-60, KB, Hep G2, and SK-Mel2 cancer cell lines showed the moderate cytotoxic activity of compound 3 (IC 50 values ranging from 51.7 to 78.3 µg/mL) to all cells, while compound 4 showed selective effect only against HL-60 cells (IC 50 61.5 µg/mL). This is the first report of cytotoxic activity of pomolic acid 3β-acetate (3) toward all tested cancer cell lines, and also the first report of cytotoxicity of rotungenic acid (4) against LU-1, HL-60, KB, Hep G2, and SK-Mel2 cancer cell lines. The methanol extract of chaga mushroom {Inonotus obliquus (Ach. ex Pers.) Pilát} exhibited the strongest cytotoxic effects against HL-60 and LU-1 (32.2 and 38.0 µg/mL, respectively), and modest cytotoxic effects against SW480 (41.3 µg/mL), HepG2 (51.3 µg/mL), KB (57.0 µg/mL), and LNCaP (57.7 µg/mL). We conclude that compounds 3 and 4 from H. pilulifera may be useful in further investigation for anticancer agent discovery and chaga could be used as a natural anticancer remedy against promyelocytic leukemia and lung adenocarcinoma.