INTRODUCTION: We performed a meta-analysis to evaluate the effect of intravesical mitomycin compared with gemcitabine on the treatment of non-muscle invasive bladder cancer. METHODS: A systematic literature search up to November 2021 was done and 6 studies included 389 subjects with non-muscle invasive bladder cancer at the start of the study; 197 of them were provided with intravesical-mitomycin and 192 with intravesical gemcitabine. The studies reported the relationships about the effect of intravesical mitomycin compared with gemcitabine on the treatment of non-muscle invasive bladder cancer. We calculated the odds ratio (OR) with 95% confidence intervals (CIs) to assess the effect of intravesical mitomycin compared with gemcitabine on the treatment of non-muscle invasive bladder cancer using the dichotomous method with a random or fixed-effect model. RESULTS: Intravesical mitomycin had significantly higher recurrence rates (OR, 2.41; 95% CI, 1.43-4.08, p=0.001) and chemical cystitis (OR, 4.39; 95% CI, 2.27-8.51, p<0.001) compared to intravesical gemcitabine in subjects with non-muscle invasive bladder cancer. However, intravesical mitomycin had no significant difference in its effect on hematuria (OR, 1.71; 95% CI, 0.68-4.33, p=0.26), skin reaction (OR, 2.04; 95% CI, 0.59-7.07, p=0.26), and liver and kidney functions damage (OR, 1.96; 95% CI, 0.35-10.96, p=0.44) compared to intravesical gemcitabine in subjects with non-muscle invasive bladder cancer. CONCLUSIONS: Intravesical mitomycin had significantly higher recurrence rates and chemical cystitis and no significant difference in its effect on hematuria, skin reaction, and liver and kidney functions damage compared to intravesical gemcitabine in subjects with non-muscle invasive bladder cancer. Further studies are required to validate these findings.