Phellinus linteus (PL) and ginseng (Panax ginseng, PG) have been widely used as traditional herbal medicines in East Asia. In this study, we evaluated whether the extract of P. linteus grown on ginseng (PGP) exhibited an more enhanced anti-proliferative activity on HT-29 human colon carcinoma cells than PL or PG extract. PGP EtOAc extract inhibited HT-29 cancer cell viability stronger than PG or PL EtOAc extract. FACS analysis revealed that PGP EtOAc extract increased sub-G1 (apoptotic) HT-29 cell population. The nuclear structures of HT-29 cells were disrupted, resulting in apoptotic fragments (45 kDa) of lamin B after treating PGP EtOAc extract. PGP EtOAc extract induced activation of caspase-8 and -9 in HT-29 cells. These results suggest that the PGP EtOAc extract has a direct anti-cancer effect through apoptosis and cell cycle blockade in HT-29 human colon carcinoma cells.