Colorectal cancer (CRC) is one of the deadliest cancers globally, ranking as the third most prevalent and second most lethal malignancy worldwide. The standard treatment for CRC typically involves a combination of surgery, radiotherapy, and chemotherapy. Despite advancements in CRC treatment, the prognosis remains unsatisfactory, primarily due to unclear mechanisms underlying tumorigenesis and the aggression of CRC. The aberrant activation of the PI3K/AKT pathway is frequently implicated in the initiation, progression, and metastasis of CRC. Studies have demonstrated that shikonin (SK) exerts anti-cancer effects. In this study, we evaluated the anti-tumor activities of a series of semi-synthesized SK derivatives against CRC cells. Our findings revealed that the SK derivative (M12) significantly inhibited the proliferation and colony formation of CRC cells, reduced cell migration, and induced apoptosis. Mechanistically, M12 enhanced the production of reactive oxygen species and downregulated the mitochondrial membrane potential, ultimately leading to mitochondrial apoptosis. Furthermore, M12 exhibited anti-CRC effects by modulating the PI3K/AKT signaling pathway and significantly suppressed tumorigenicity without causing notable adverse effects in mice. Therefore, targeting the PI3K/AKT pathway could be a promising treatment for CRC. M12 appears to be a promising candidate for the effective and safe treatment of CRC.