Acetylshikonin, a natural naphthoquinone derivative compound from Lithospermum erythrorhyzon, has been reported to kill bacteria, suppress inflammation, and inhibit tumor growth. However, the effect of acetylshikonin on human chronic myelocytic leukemia (CML) cells apoptosis and its detailed mechanisms remains unknown. The purpose of the present study was to investigate whether acetylshikonin could inhibit proliferation or induce apoptosis of the K562 cells, and whether by regulating the NF-κB signaling pathway to suppress the development of CML. K562 cells were treated with serial diluted acetylshikonin at different concentrations. Our data showed that K562 cell growth was significantly inhibited by acetylshikonin with an IC₅₀ of 2.03 μM at 24 h and 1.13 μM at 48 h, with increased cell cycle arrest in S-phase. The results of annexin V-FITC/PI and AO/EB staining showed that acetylshikonin induced cell apoptosis in a dose-dependent manner. K562 cells treated with acetylshikonin underwent massive apoptosis accompanied by a rapid generation of reactive oxygen species (ROS). Scavenging the ROS completely blocked the induction of apoptosis following acetylshikonin treatment. The levels of the pro-apoptotic proteins Bax, cleaved caspase-9, cleaved PARP and cleaved caspase-3 increased with increased concentrations of acetylshikonin, while the level of the anti-apoptotic protein Bcl-2 was downregulated. The levels of Cyt C and AIF, which are characteristic proteins of the mitochondria-regulated intrinsic apoptotic pathway, also increased in the cytosol after acetylshikonin treatment. However, the mitochondrial fraction of Cyt C and AIF were decreased under acetylshikonin treatment. In addition, acetylshikonin decreased Bcr-Abl expression and inhibited its downstream signaling. Acetylshikonin could lead to a blockage of the NF-κB signaling pathway via decreasing nuclear NF-κB P65 and increasing cytoplasmic NF-κB P65. Moreover, acetylshikonin significantly inhibited the phosphorylation of IkBα and IKKα/β in K562 cells. These results demonstrated that acetylshikonin significantly inhibited K562 cell growth and induced cell apoptosis through the mitochondria-regulated intrinsic apoptotic pathway. The mechanisms may involve the modulating ROS accumulation, inhibition of NF-κB and BCR-ABL expression. The inhibition of BCR-ABL expression and the inactivation of the NF-κB signaling pathway caused by acetylshikonin treatment resulted in K562 cell apoptosis. Together, our results indicate that acetylshikonin could serve as a potential therapeutic agent for the future treatment of CML.