Maple syrup urine disease (MSUD) is an autosomal recessive metabolic disorder affecting branched-chain amino acids. Mutations in the BCKDHA, BCKDHB, and DBT gene impair the branched-chain alpha-ketoacid dehydrogenase (BCKD) complex, resulting in the accumulation of branched-chain amino acids and branched-chain alpha-ketoacid in tissues and plasma. This leads to mental and physical retardation, feeding problems, and a maple syrup odor in the urine. In this study, we describe the clinical and biochemical manifestations of a sporadic mutation in a neonate with classic MSUD. Analysis of the BCKDHA gene revealed a compound heterozygous mutation consisting of two novel missense mutations (p.L103P and p.R265P). Viewing the protein with PyMOL indicated that the p.L103P and p.R265P mutations were, respectively, located in the helical region and core domains of the BCKD's Ela component. The p.L103P mutation affected the hydrophobic cores and is predicted to shorten the helix; the p.R265P mutation can predictably affect the cofactor binding site by ligating the associated manganese ion. In conclusion, we identified two novel missense mutations in the BCKDHA gene in a Chinese patient with MSUD.