Bladder pain syndrome/interstitial cystitis (BPS/IC) is a common debilitating disease and there has not been consistently effective treatment. We aimed to evaluate all available literature regarding the efficacy and safety of sacral neuromodulation (SNM) for refractory BPS/IC. A comprehensive search of Pubmed, Web of Science and Cochrane Library through May 2016 was conducted. A total of 17 studies enrolling 583 patients were identified. Pooled analyses demonstrated that SNM was associated with great reduction in pelvic pain (weighted mean difference [WMD] -3.99; 95% confidence interval [CI] -5.22 to -2.76; p < 0.00001), Interstitial Cystitis Problem and Symptom Index scores (WMD -6.34; 95% CI -9.57 to -3.10; p = 0.0001; and WMD -7.17; 95% CI -9.90 to -4.45; p < 0.00001, respectively), daytime frequency (WMD -7.45; 95% CI -9.68 to -5.22; p < 0.00001), nocturia (WMD -3.01; 95% CI -3.56 to -2.45; p < 0.00001), voids per 24 hours (WMD -9.32; 95% CI -10.90 to -7.74; p < 0.00001) and urgency (WMD -1.08; 95% CI -1.79 to -0.37; p = 0.003) as well as significant improvement in average voided volume (WMD 95.16 ml; 95% CI 63.64 to 126.69; p < 0.0001). The pooled treatment success rate was 84% (95% CI 76% to 91%). SNM-related adverse events were minimal. Current evidence indicates that SNM might be effective and safe for treating refractory BPS/IC.