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NFU1 deficiency is a rare metabolic disorder affecting iron–sulfur cluster synthesis, an essential pathway for lipoic acid-dependent enzymatic activities and mitochondrial respiratory chain complexes. It is a little-known cause of pulmonary arterial hypertension (PAH), while PAH is a prominent feature of the disease. We herein report on a female infant diagnosed as having idiopathic PAH since 1 month of age, who did not respond to bosentan plus sildenafil. NFU1 deficiency was only suggested and confirmed at 10 months of age when she demonstrated neurological deterioration along with high glycine levels in body fluids. Unexplained PAH in early infancy should prompt clinicians to perform amino acid chromatography searching for high glycine levels. Early recognition will avoid further invasive procedures and enable appropriate genetic counseling to be offered. No effective treatment is currently able to prevent the fatal course of this metabolic condition.