A 22-day-old female infant was referred to our hospital due to unusual urine odor suspecting inborn error of metabolism. Physical examination revealed a stuporous and hypotonic infant with poor reflexes. Intravenous thiamine and high glucose along with appropriate protein were given under the suspicion of maple syrup urine disease (MSUD), which was confirmed by blood and cerebrospinal fluid amino acid assays, and urinary organic acid assay. Progressive neurological deterioration was observed despite the non-invasive treatment. So, we performed pump assisted continuous arteriovenous haemofiltration (CAVHF). Dramatic improvement in neurological function was observed hours after initiation of CAVHF, along with decrease in the level of isoleucine, leucine and valine. In our experience, CAVHF is a well-tolerated procedure for managing the acute phase of neonatal MSUD. Further study on indications, duration of treatment, and preventing complications is needed.