Background: The aim of this study was to assess the effectiveness of neuroendoscopy compared with non-neuroendoscopic procedures for treating patients with arachnoid membrane cysts in the lateral ventricles. Methods: The medical records of 28 patients with arachnoid membrane cysts in the lateral ventricles who were treated with neuroendoscopy and 39 such patients treated with non-neuroendoscopic techniques using classic treatment procedures were reviewed. The neuroendoscopic approach combined craniotomy, corticectomy, lesion resection and cyst ventriculostomy or cyst cisternostomy to restore normal cerebrospinal fluid circulation. The non-neuroendoscopic techniques included craniotomy, corticectomy, and lesion resection performed under a microscope. Clinical outcomes of symptoms and cyst size change on imaging were compared between the two treatment groups during follow-up (range: 1-5 years). Results: Patients in the neuroendoscopy group had significantly less blood loss (P < 0.001) and shorter operative time (P < 0.001), better marked improvement in symptoms (64.3% vs. 5.1%, respectively), and a higher total resection rate (92.9% vs. 66.7%; P = 0.011) compared with the patients in the non-neuroendoscopy group. In the neuroendoscopy group there was no cyst recurrence whereas in the non-neuroendoscopy group 8 (20.5%) patients had cyst recurrence. However, all patients in the neuroendoscopy group had postoperative transient fever and 8 (28.6%) patients had subdural fluid accumulation which was treated and subsequently resolved during follow-up. These symptoms did not occur in the non-neuroendoscopy group. Conclusion: We found that neuroendoscopic therapy for arachnoid cysts in the lateral ventricles was more efficacious than non-neuroendoscopic methods. Our results indicate that neuroendoscopy may produce better clinical outcomes than non-neuroendoscopic procedures in treating patients with arachnoid cysts in the lateral ventricles.