Backgrounds: Statin therapy is widely used for the management of dyslipidemia and prevention of cardiovascular diseases. However, there is growing concern about its potential effects on bone metabolism markers and mineral density. This systematic review and meta-analysis aimed to investigate the effect of statin therapy on these parameters. Methods: PubMed/MEDLINE, Scopus, and Clarivate Analytics Web of Science databases were searched from inception to August 2023, using MESH terms and keywords. Results: After screening 2450 articles, 16 studies that met the inclusion criteria were included, of which 12 randomized controlled trials (RCTs) were used for meta-analysis. The findings showed that statin therapy significantly reduced bone-specific alkaline phosphatase (B-ALP) levels (WMD = -1.1 U/L; 95% CI -2.2 to -0.07; p = 0.03; I2 = 0%,), and bone mineral density (BMD) at different sites (WMD = -0.06 g/cm2; 95% CI -0.08 to -0.04; P < 0.001; I2 = 97.7%, P<0.001). However, this treatment did not have a significant effect on osteocalcin, serum C-terminal peptide of type I collagen (S-CTx), serum N-telopeptides of type I collagen (NTx) concentration, or overall fracture risk. Conclusion: This systematic review and meta-analysis provide evidence that statin therapy is associated with a significant reduction in B-ALP levels and BMD at different sites of the skeleton. Further studies are needed to investigate the long-term effects of statin therapy on bone health and to identify the potential underlying mechanisms.