This study analyzed the effects of topical anti-glaucoma medications on the surgical outcomes of endoscopic dacryocystorhinostomy (EDCR) in nasolacrimal duct obstruction (NLDO). This retrospective study included patients who underwent EDCR for NLDO between September 2012 and April 2021. Thirty patients with topical anti-glaucoma medications and 90 age- and sex-matched controls were included. The success rate of EDCR was higher in the control group than in the anti-glaucoma group (97.8% vs. 86.7%, p = 0.034). Univariate and multivariate logistic regression analyses identified prostaglandin analogs as the most influential risk factor for EDCR success among anti-glaucoma medication ingredients (p = 0.005). The success rate of the group containing all four anti-glaucoma medication ingredients was statistically significant (p = 0.010). The success rate was significantly different in the group of patients who used anti-glaucoma medication for >24 months (p = 0.019). When multiplying the number of drug ingredients by the duration in months, the group > 69 showed a significantly decreased success rate (p = 0.022). Multivariate logistic regression analysis identified the number of anti-glaucoma medications as the most significant risk factor for EDCR success (odds ratio, 0.437; 95% confidence interval, 0.247 to 0.772; p = 0.004). The authors suggest that the anti-glaucoma medications might cause NLDO and increase the failure rate after EDCR. Therefore, when performing EDCR in patients using topical anti-glaucoma medications, surgeons should consider the possibility of increased recurrence after EDCR in clinical outcomes.