Abstract Background Magnesium has a regulatory role in the excitability of cell membranes, and is also a cofactor in the phosphorylation of thiamine. Hypomagnesemia has been associated with coronary vasospasm, but its role in cerebrovascular pathology is controversial, and cerebral vasospasm exclusively attributable to hypomagnesemia has not been reported in humans. Case presentation We report the case of a 51-year-old man in whom uncontrollable vomiting, treatment with omeprazole and thiazide, and renal impairment lead to a severe hypomagnesemia (magnesium below the level of detection in blood tests), which secondarily caused Wernicke’s encephalopathy and vasospasm in multiple cerebral arteries (seen with cerebral angiography and CT angiography) that presented with a complete right hemisphere neurological deficit. These disturbances completely resolved when magnesium levels were normalized and subsequent neuroimaging tests confirmed the resolution of angiographic changes. Conclusion Our case suggests that hypomagnesemia should be considered in the differential diagnosis of patients with neurological symptoms and predisposing causes.