Aims Low-intensity extracorporeal shock wave therapy (Li-ESWT) has been applied in urolithiasis and some chronic diseases. We performed a systematic review and meta-analysis to assess the efficacy of Li-ESWT for the treatment of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). Methods A comprehensive search of MEDLINE, Web of Science, EMBASE, and the Cochrane Library to January 6, 2019 was performed for randomized controlled trials (RCTs) reporting on patients with CP/CPPS treated with Li-ESWT compared with the sham group. Outcomes were evaluated based on the National Institutes of Health Chronic Prostatitis Symptom Index (NIH-CPSI). The quality assessment of included studies was performed by the Cochrane System. Results Six publications involving five RCTs with 280 patients were assessed in this review. NIH-CPSI total score, pain domain and quality of life (QOL) were significantly better in the Li-ESWT group than those in the control group at the endpoint (P < 0.00001, P = 0.003, and P < 0.00001), 4 weeks (P < 0.00001, P = 0.0002 and P < 0.00001) and 12 weeks (P < 0.00001, P < 0.00001, and P = 0.0002) after the treatment. For urinary score, significant difference existed at 12 weeks after the treatment (P = 0.006). At 24 weeks after treatment, there was no significant difference between the two groups in NIH-CPSI total score (P = 0.26), pain domain (P = 0.32), urinary score (P = 0.07), and QOL (P = 0.29). Conclusions Li-ESWT showed great efficacy for the treatment of CP/CPPS at the endpoint and during the follow-up of 4 and 12 weeks, though the efficacy of 24-week follow-up was not significantly different due to insufficient data. Generally, Li-ESWT is a promising minimal invasive method for the treatment of CP/CPPS.