Citrullinemia is a urea cycle disorder caused by deficiency of argininosuccinate synthetase. Late onset forms can remain undiscovered until a decompensation that can resemble encephalitis. Herein, we report a 14-year old patient with suspected encephalitis with fluctuating episodes of confusion. EEG mainly showed bilateral slowing with some spikes plus spike waves; and was interpreted as suspicious for encephalitis. Brain MRI was normal. Leukocytes in CSF were slightly elevated. Treatment for a CNS infectious disease was begun. Symptoms did not resolve and there were several episodes of confusion, so a repeat lumbar puncture was performed according to a standardized protocol including an amino acid profile. An elevation of citrulline in CSF was found, which ultimately led to the diagnosis of a late onset citrullinemia. The establishment of this diagnosis will protect the patient from the sequelae of unrecognized and thus untreated episodes of hyperammonemia. Thus, following a standardized lumbar puncture protocol can be essential to detect patients with otherwise unrecognized underlying metabolic disorders that are not suspected because of clinical symptoms. In addition, it is important to stress that an ammonia concentration should be determined in any patient with neurological signs like confusion.