Abstract Background Varicocele is one of the most common causes of reversible male infertility, and 15% of the varicocele patients with normal semen analysis are diagnosed as infertile. According to the current guidelines, varicocelectomy is indicated based on abnormal sperm parameters and not abnormal DNA fragmentation index (DFI) values. Thus, in this study, we performed a meta-analysis of the effects of varicocelectomy on the DFI and other conventional sperm parameters, and determined whether DFI could be used to indicate varicocelectomy for varicocele patients. Results Through an electronic search of the PubMed, Scopus, EBSCO, and Cochrane databases, we included 7 prospective studies including a total of 289 patients in this meta-analysis. The results showed that varicocelectomy significantly reduced DNA fragmentation (mean difference: − 6.86; 95% confidence interval [CI]: − 10.04, − 3.69; p < 0.00001) and improved sperm concentration (mean difference: 9.59; 95% CI: 7.80, 11.38; p < 0.00001), progressive motility (mean difference: 8.66; 95% CI: 6.96, 10.36; p < 0.00001), and morphology (mean difference: 2.73; 95% CI: 0,65, 4.80; p = 0.01). Conclusion Varicocelectomy reduced DNA fragmentation and improved sperm concentration, progressive motility, and morphology. Additionally, the analysis showed that an abnormal DFI measurement should be considered as an indication for varicocelectomy.