Background: One of the most dangerous side effects of joint replacement for the hip, knee, shoulder, and elbow is prosthesis joint infection (PJI). Polymerase chain reaction (PCR) has been considered a promising method for PJI diagnosis due to its short diagnostic time and high sensitivity. Although several PCR methods such as multiplex PCR and broad-range PCR are useful diagnostic methods for detecting microorganisms causing PJI, values of different PCR methods for the diagnosis of PJI remain unclear. Thus, the objective of this study was to perform a meta-analysis of different PCR methods in the diagnosis of PJI to determine their diagnostic characteristics including sensitivity and specificity. Methods: The following data were extracted: PCR method, number of patients, sample site and type, diagnosis standard, true positive, false positive, false negative, and true negative. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were calculated. Meta-regression analysis was conducted to assess heterogeneity. Subgroup analysis was also performed to assess effects of several variables on meta-analysis results. Results: The current study showed that pooled sensitivity and pooled specificity were 0.70 (95% CI: 0.67-0.73) and 0.94 (95% CI: 0.92-0.95), respectively. Results of subgroup analysis indicated that sequencing method showed the lowest sensitivity (0.63, 95% CI: 0.59-0.67). However, after excluding studies using tissue samples directly, sequencing method showed higher sensitivity (0.83, 95% CI: 0.73-0.90) than other PCR methods (0.74, 95% CI: 0.69-0.78). Conclusions: The main significance of this study was that we attempted to classify accuracies of several PCR methods and found that sequencing with a reliable sampling method could be used as an early screening strategy for PJI. Further comparisons for PCR technologies are needed to evaluate their cost effectiveness and diagnostic procedures, not just diagnostic values, to discover the optimal one for PJI diagnosis.