Background Hyponatremia can be developed during hysteroscopic surgery with electrolyte-free irrigation fluid. We experienced severe hyponatremia with postoperative seizures and confirmed mild brain edema. Case presentation A quadragenarian female patient underwent a 2-h hysteroscopic myomectomy with electrolyte-free fluid for uterine distension under general anesthesia. Plasma sodium level of 84.1 mmol/L 100 min after the start of surgery indicated excessive absorption of the irrigation fluid. Acute severe hyponatremia was diagnosed with significant edema in the conjunctiva, lip, and extremities. She was treated with a continuous infusion of hypertonic saline. However, seizures and cerebral edema developed 7 h later. The patient recovered without neurological deficits at postoperative day 2. Conclusion The electrolyte-free irrigation fluid can be absorbed rapidly during hysteroscopic surgery. Its interruption with hyponatremia should be considered against prolonged surgery. Especially under general anesthesia, caution should be exercised because the typical symptoms of hyponatremia such as nausea and confusion are blinded.