OBJECTIVE Bypass surgery is the most common treatment for moyamoya disease (MMD), but there is controversy over which surgical modality is best. The objective of this study was to evaluate the clinical outcome of patients with MMD after undergoing different surgical modalities. METHODS A series of 696 consecutive MMD patients treated between June 2009 and May 2015 were screened in this prospective cohort study. Patients who did not undergo revascularization surgeries and those who underwent different surgical modalities in bilateral hemispheres were excluded. Finally, 529 patients who were observed for at least 12 months were included: 438 patients underwent unilateral surgery, and 91 patients underwent bilateral surgery. Of these, 241 patients underwent direct bypass (DB); 81, a combined bypass (CB); and 207, an indirect bypass (IB). Three clinical outcomes were evaluated and compared between surgical groups: recurrent stroke events, modified Rankin Scale (mRS) scores, and change in the main symptoms. RESULTS The mean follow-up period was 40 months. During the follow-up period, recurrent stroke was observed in 43 patients, including 15 patients with hemorrhage, 26 patients with ischemia (transient ischemic attack in 19 patients and infarction in 7 patients), and 2 patients with both hemorrhage and cerebral infarction. Kaplan-Meier analysis showed that patients who underwent a CB or DB had a longer ischemia-free time than those who underwent IB (p = 0.013); however, there was no significant difference in the hemorrhage-free time between the different surgical modalities (p = 0.534). A good neurological status (mRS score = 2) was achieved in 495 patients (93.6%) and was significantly achieved by more children (98.2%) than adults (92.3%; p = 0.022). Surgical modalities were not significantly associated with outcome neurological status (p = 0.860). Moreover, improvement in symptoms was observed in 449 patients (84.9%) and was also significantly more common in children (93.0%) than in adults (82.7%; p = 0.006). No significant difference was observed between the different surgical modalities (p = 0.548). CONCLUSIONS CB and DB are more effective at preventing recurrent ischemic strokes than IB. However, there is no evidence that these 3 surgical modalities demonstrate significant differences in preventing recurrent hemorrhage.