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Catheter ablation for atrial fibrillation creates an iatrogenic atrial septal defect by transseptal puncture, which may produce a transient right-to-left shunt. We encountered a 44-year-old man who presented with de novo migraine-like headache after cryoballoon ablation for atrial fibrillation. On reviewing the literature, we found additional cases in which migraine-like headache occurred within one week after the procedure and spontaneously within three months. We should recognize migraine-like headache as a potential complication of catheter ablation.