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A 9-year-old girl, diagnosed case of Fanconi anemia, presented with generalized convulsion with altered sensorium. She had fever, severe pallor, sinus tachycardia, blood pressure of 180/120 mmHg in both upper and lower limb, pan-systolic murmur of grade 2/6, abdominal bruit and bilateral papilledema. A provisional diagnosis of hypertensive encephalopathy was made and managed with continuous labetalol infusion. Detailed evaluation including magnetic resonance angiography of renal artery detected underlying atrophic and non-functioning right kidney secondary to severe renal artery stenosis on the same side. She was started with multiple antihypertensives, but her blood pressure was maintained poorly. Later on, she underwent rightsided nephrectomy. Following surgery, she was doing well and maintaining normal blood pressure without any antihypertensives. Our child is the second reported case of Fanconi anemia associated with renal artery stenosis presenting with hypertensive encephalopathy.