Context: Medicinal plants can be used as an option for the prevention and reduction of cancer cell resistance and its side effects. Sisyrinchium palmifolium L. is thought to have anti-cancer activity with a compound content of 1,4-naphthoquinone. Aims: To determine the effect of S. palmifolium extract (SPE) with the main compound 1,4-naphthoquinone on Ki-67 expression by in vivo, and CDK1, CDK2, and CDK4 activity by in silico in colonic epithelial cells of BALB/ c mice induced by azoxymethane (AOM) dextran sodium sulfate (DSS). Methods: Dayak onion (S. palmifolium) was extracted using 96% ethanol as a solvent. The S. palmifolium extract was then made into tablet form by the wet granulation method. Mice that had been induced with AOM-DSS were given S. palmifolium extract therapy. Twenty samples were used, which were divided into five groups. Mice colon tissue was assessed using Ki-67 immunohistochemistry. This study also used the in silico method to see the effect of 1,4-naphthoquinone compounds from S. palmifolium extract on the expression of CDK1, CDK2 and CDK4 with PDB codes 6GU6, 6GUC, and 1GIH. Results: Ki-67 expression values were 26 ± 6.51 cells at low dosages, 15 ± 1.73 cells at moderate doses, and 11 ± 1.04 cells at high doses. Between the test groups, there was a statistical differences (p<0.05) with the Post Hoc Mann-Whitney test. At the 6GUC receptor, the mean rerank score of the 1,4-naphtoquinone molecule, which was closest to the native ligand, was -54.6572 ± 2.2722 and -90.5455 ± 1.6524kcal/mole. The steric bond on the amino acid lys 33 (A), which exclusively occurs at the 6GUC receptor, was the only commonality of contact. Conclusions: 1,4-Naphthoquinone from Sisyrinchium palmifolium L. extract could decrease Ki-67 expression by in vivo, which cloud induce a decrease in epithelial cells proliferation in colon cancer, but has no potential as an inhibitor activity of CDK1, CDK2, and CDK4 by in silico.