Background: We conducted a meta-analysis to compare the efficacy and toxicity of scheduled intravesical gemcitabine (GEM) and Bacille Calmette-Guerin (BCG) for Ta and T1 non-muscle invasive bladder cancer (NMIBC). Methods: The database search was performed in Ovid Medline, Embase, Web of Science, Cochrane Library from the commencement of the database to July 7, 2020. Trials using immediate instillation were excluded and we present the included studies in accordance with the PRISMA 2020 reporting checklist. The data extracted was analyzed using Stata 11.0 software. Results: Six studies of 466 patients comparing GEM and BCG were finally included. No significant difference was detected between GEM and BCG group in recurrence free survival [hazard ratio (HR) =0.80, 95% confidence interval (95% CI), 0.46-1.37, P=0.410], progression free survival (HR =0.82, 95% CI, 0.38-1.77, P=0.621), and total adverse events [odds ratio (OR) =0.70, 95% CI, 0.38-1.29, P=0.253). However, patients receiving GEM treatment are less likely to develop urinary adverse events, such as dysuria (OR =0.50, 95% CI, 0.29-0.87) and hematuria (OR =0.40, 95% CI, 0.18-0.91). We performed subgroup analysis and found that the effects of GEM and BCG were similar even on patients with high recurrence risk tumor. Sensitivity analysis showed the robustness of the results. Discussion: Scheduled intravesical GEM instillation has a similar effect with BCG instillation in preventing NMIBC recurrence and progression, but GEM therapy causes a lower incidence of dysuria and hematuria than BCG. GEM may be an alternative therapy for BCG. However, the results should be treated with caution due to the low to moderate quality of the included studies.