Background and purposeAlthough numerous studies have shown that positive surgical margin (PSM) is linked to biochemical recurrence (BCR) in prostate cancer (PCa), the research results have been inconsistent. This study aimed to explore the association between PSM and BCR in patients with PCa following radical prostatectomy (RP).Materials and methodsIn accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), PubMed, EMBASE and Wan Fang databases were searched for eligible studies from inception to November 2017. The Newcastle–Ottawa Scale was used to assess the risk of bias of the included studies. Meta-analysis was performed by using Stata 12.0. Combined hazard ratios (HRs) and their corresponding 95% confidence intervals (CIs) were calculated using random-effects or fixed-effects models.ResultsUltimately, 41 retrospective cohort studies of high quality that met the eligibility criteria, comprising 37,928 patients (94–3294 per study), were included in this meta-analysis. The results showed that PSM was associated with higher BCR risk in both univariate analysis (pooled HR = 1.56; 95% CI 1.46, 1.66; p < 0.001) and multivariate analysis (pooled HR = 1.35; 95% CI 1.27, 1.43; p < 0.001). Moreover, no potential publication bias was observed among the included studies in univariate analysis (p-Begg = 0.971) and multivariate analysis (p-Begg = 0.401).ConclusionsOur meta-analysis demonstrated that PSM is associated with a higher risk of BCR in PCa following RP and could serve as an independent prognostic factor in patients with PCa.Electronic supplementary materialThe online version of this article (10.1186/s12957-018-1433-3) contains supplementary material, which is available to authorized users.