Metabolic myopathies represent a small percentage of rhabdomyolysis causes that could lead to acute kidney injury (AKI). This could be prevented if this condition is suspected and timely treated. Carnitine palmityl transferase (CPT) deficiency is the most frequent metabolic myopathy and should be considered whenever recurrent myoglobinuria is suspected, and distinguished from the second frequent one, McArdle disease. We present a case of a patient with two medically misinterpreted episodes of AKI in whom the subsequent diagnosis of CPT deficiency was established based on high index of clinical suspicion and correlation of clinical manifestations to specific metabolic defects. Application of simple measures and lifestyle changes improved our patient's life quality and prevented potential new life-threatening complications.