Objective: Brainstem arteriovenous malformations (AVMs) are rare lesions with a high risk of intracranial hemorrhage and are challenging to treat. We present our experience of endovascular embolization with Onyx in these aggressive lesions. Materials and methods: Between 2007 and 2016, 13 patients with brainstem AVMs were embolized with Onyx at our center. Twelve patients presented with intracranial hemorrhage and one with headache. Retrospective examinations of patient demographics, clinical presentation, angiographic features, treatment modalities, postoperative complications and outcomes were carried out. Results: The AVMs were in the midbrain in 10 patients (one anterior and nine posterior or dorsal), in the posterior pons in two and pontomedullary in one. Complete occlusion was achieved in three patients. Gamma knife radiosurgery was performed in six patients who were near-completely or partially embolized. Postoperative complications, including five cases of ischemia and one case of hemorrhage, resulted in four cases of neurological deterioration and two deaths. Clinical follow-up was obtained in 10 patients at a mean period of 45.2 months (range 3 to 93 months). During the follow-up, good clinical outcomes were observed in seven patients with posterior or dorsal midbrain AVMs, and one patient with a posterior pons AVM that was partially occluded died of intracranial hemorrhage. Conclusion: Endovascular embolization for brainstem AVM with Onyx is a technical challenge and the reflux of Onyx may cause severe complications. Individualized treatment is needed based on the specific subtype of brainstem AVM.