Both primary pulmonary artery hypertension (PPAH) and autoimmune polyendocrine syndrome (APS) are rare disorders in children. We report a boy who was diagnosed with severe PPAH at 12 years of age. He was treated with prostacyclin for 6 years, briefly with adjunct bosentan, and eventually sildenafil was added. Six years later, after his diagnosis of PPAH, he developed APS in the form of hyperthyroidism and type 1 diabetes mellitus. No mutations were identified through genetic testing of bone morphogenetic protein receptor type II and the autoimmune-regulator gene. To our knowledge this is the first description of the combination of these two extremely rare diseases in a child.