A male neonate was admitted on postnatal day 1 with persistent pulmonary hypertension. Despite aggressive treatment, the pulmonary hypertension progressively worsened, leading to early right heart failure. Whole-exome sequencing of the family revealed compound heterozygous mutations c.192del and c.192_193del in the NDUFAF2 gene, inherited from each parent, meeting the pathogenic variant criteria of the American College of Medical Genetics and Genomics. Autopsy showed pulmonary artery dilation and myocardial hypertrophy, with no evidence of alveolar capillary dysplasia on lung tissue electron microscopy. Mutations in the NDUFAF2 gene are associated with mitochondrial complex I deficiency. This is the first reported case associating NDUFAF2 mutations with neonatal primary pulmonary hypertension, providing new genetic evidence for this condition and highlighting the importance of genetic and pathological studies in severe neonatal diseases.