Objective To explore the clinical phenotype and genotype of leukoencephalopathy with thalamus and brainstem involvement and high lactate caused by a novel mutation of EARS 2 gene. Methods The clinical data of leukoencephalopathy with thalamus and brainstem involvement and high lactate in a neonate were retrospectively analyzed, and the related literature was reviewed. Results A 26 -hour-old female presented with poor response, convulsions and refractory hyperlactemia. Head MRI during pregnancy showed absence of corpus callosum. The heterozygous nonsense mutation of c.1294C>T in exon 7 and heterozygous missense mutation of c.971 G>T in exon 5 of EARS2 gene were detected by whole exon sequencing, which were come from her father and mother respectively. No mitochondrial gene variation was found in the child by the second generation sequencing of mitochondrial gene, but a heterogeneous deletion mutation of mitochondrial gene MTND 1- 1 * was found in the child and her mother by MLPA test. Conclusion New nonsense mutation of c. 1294 C>T and missense mutation of c.971G>T in EARS2 nuclear gene were found in leukoencephalopathy with thalamus and brainstem involvement and high lactate.