The aim of this study was to describe skew deviation and vertical nystagmus as the initial signs for basilar artery thrombosis, a life-threatening disease. A 51-year-old woman complained of vertical diplopia for more than 20 h. A computed tomography of the brain was normal, but subsequently the patient developed additional symptoms including nausea, ventilation problems (dyspnoea) and somnolence. Neuro-ophthalmological evaluation revealed a skew deviation and a vertical nystagmus. Magnetic resonance imaging allowed the diagnosis of basilar artery occlusion. An emergency intervention with cerebral catheter angiography and local intra-arterial thrombolysis was performed. Total recanalization of the basilar artery was achieved resulting in a complete neurological recovery, including the skew deviation and nystagmus. This rare case of skew deviation associated with basilar artery occlusion was a diagnostic challenge and highlights adequate differential diagnosis. Skew deviation is an important clinical sign. In this patient it was the key to a correct diagnosis enabling an immediate and successful intervention.