Abstract Introduction CNS cavernomas are a type of raspberry-shaped vascular malformations that are typically asymptomatic, but can result in haemorrhage, neurological injury, and seizures. Here, we present a rare case of a brainstem cavernoma that was surgically resected whereafter an upbeat nystagmus presented postoperatively. Case report A 42-year old man presented with sudden-onset nausea, vomiting, vertigo, blurred vision, marked imbalance and difficulty swallowing. Neurological evaluation showed bilateral ataxia, generalized hyperreflexia with left-sided predominance, predominantly horizontal gaze evoked nystagmus on right and left gaze, slight left labial asymmetry, uvula deviation to the right, and tongue deviation to the left. MRI demonstrated a 13-mm cavernoma with haemorrhage and oedema in the medulla oblongata. Surgery was performed via a minimal-invasive, midline approach. Complete excision was confirmed on postoperative MRI. The patient recovered well and became almost neurologically intact. However, he complained of mainly vertical oscillopsia. The videonystagmography revealed a new-onset spontaneous upbeat nystagmus in all gaze directions, not suppressed by fixation. An injury of the rarely described intercalatus nucleus/nucleus of Roller is thought to be the cause. Conclusion Upbeat nystagmus can be related to several lesions of the brainstem, including the medial longitudinal fasciculus, the pons, and the dorsal medulla. To our knowledge, this is the first case of an iatrogenic lesion of the nucleus intercalatus/nucleus of Roller resulting in an upbeat vertical nystagmus. For neurologists, it is important to be aware of the function of this nucleus for assessment of clinical manifestations due to lesions within this region.