Purpose: This nationwide longitudinal cohort study aims to investigate the association between Moyamoya disease (MMD) and subsequent development of secondary glaucoma. Methods: The records of patients with MMD and a control group between 2002 and 2022 were extracted from the Korean National Health Insurance Service database. Cases with MMD diagnosed in the first two years of the study period and cases with any glaucoma diagnosed prior to MMD were excluded. Cox proportional hazard models were used to assess the association of MMD with secondary glaucoma. Kaplan–Meier survival analysis with a log-rank test was performed to compare the incidence probability of secondary glaucoma between MMD patients and controls. Results: A total of 36,432 patients with a diagnostic code for MMD and age-/sex-matched non-MMD controls (n = 346,769) were included. Cox regression analysis showed that MMD was associated with increased risk of secondary glaucoma (adjusted hazard ratio, 2.42; 95% confidence interval, 1.84–3.18; p < 0.001). Other risk factors included male sex, older age, hypertension, diabetes, and peripheral artery disease. The incidence probability of secondary glaucoma was significantly higher in MMD patients compared to controls (p < 0.001). Conclusions Patients with MMD face elevated risk of developing secondary glaucoma, indicating that MMD may be a potential risk factor for secondary glaucoma.