Background: The aim of the study was to systematically review the relevant studies to assess the role of fluorescence in situ hybridization (FISH) test for predicting patient response to Bacillus Calmette-Guerin (BCG) therapy after transurethral resection of bladder tumor (TURBT). Methods: We searched PubMed, Embase, and the Cochrane Library from inception to July 5, 2018, and used Quality Assessment Tool for Diagnosis Accuracy Studies (QUADAS-2) to assess the quality. We pooled sensitivity, specificity, and area under curve (AUC) of baseline and post-BCG FISH test for predicting tumor recurrence. Hazard ratio (HR) with 95% confidence intervals (95% CIs) and a Fagan nomogram were applied to assess predictive accuracy of post-BCG FISH test. Results: A total of 6 studies with 442 participants for post-BCG test and 404 participants for baseline BCG test were included. The pooled analysis for post-BCG FISH test revealed the sensitivity of 0.54 (95% CI 0.38-0.69), specificity of 0.84 (95% CI: 0.72-0.91), and area under the curve (AUC) of 0.78 (95% CI: 0.74-0.81) for predicting tumor recurrence. Patients with positive post-BCG FISH test were more likely to recur during follow-up (HR 3.95, 95% CI 2.72-5.72). The Fagan nomogram revealed the `post-test` probability of tumor recurrence increased by 29% for patients with positive post-BCG FISH test. The baseline FISH test had a pooled sensitivity of 0.70 (95% CI 0.55-0.81), specificity of 0.41 (95% CI: 0.26-0.58), and AUC of 0.60 (95% CI: 0.56-0.64) for predicting recurrence. Conclusion: The post-BCG FISH test can predict BCG failure with high specificity and patients with positive post-BCG FISH test were more likely to recur. However, the relatively low sensitivity of post-BCG FISH test and unsatisfactory performance of baseline FISH test may limit their mono-use.