Decreased expression of the tumor suppressor sirtuin 6 (SIRT6) protein plays a role in tumorigenesis. The aim of this study was to investigate the effects of SIRT6 and its underlying mechanism in colon cancer progression. As shown by immunohistochemistry, Western blotting, and the real-time polymerase chain reaction (RT-PCR), SIRT6 expression was down-regulated in colon cancer tissues and different colon cancer cell lines, and down-regulation of SIRT6 showed a negative correlation with the overall survival of colon cancer patients. To assess the effects of SIRT6 on cell proliferation, apoptosis, invasion, and migration, 3-(4,5-dimethyl-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, transwell, and wound healing assays were carried out, respectively. Results demonstrated that over-expression of SIRT6 inhibited cell proliferation, invasion, and migration and enhanced cell apoptosis. Co-immunoprecipitation (Co-IP) and Western blotting showed that up-regulation of SIRT6 increased the combined quantity of PTEN with SIRT6 proteins, and promoted the expression of PTEN and PIP2, as well as the stability of PTEN. SIRT6 also reduced the ubiquitination of PTEN and decreased protein levels of AKT1, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), mTOR, cyclin d1, and c-myc. In addition, compared with cells over-expressed SIRT6, cell apoptosis was repressed and cell proliferation and tumorigenesis were enhanced in cells with SIRT6 over-expression and PTEN knockdown. In conclusion, the present study confirms that SIRT6 functions as a tumor suppressor gene in colon cancer by modulating PTEN/AKT signaling, which may provide a novel target for the treatment of colon cancer.