[Introduction] Incontinentia pigmenti (IP) is a rare X-linked dominant genodermatosis that presents multiple disorders of the ectodermal tissues. IP is caused by mutations in the NF-kappaB essential modulator (NEMO) gene. There are a few reports of cardiovascular involvement in IP; however, fatal pulmonary hypertension (PH) in IP has seldom been reported and little is known about its etiology. We report an infant girl with IP accompanied by severe PH, and her histo-pathological findings of pulmonary artery (PA). [Case Presentation] The patient was clinically diagnosed as IP during her neonatal period based on the specific skin lesion, neonatal seizure and the family history of IP. At the age of 2 months, systolic heart murmur was pointed out, and severe PH was detected by echocardiography and cardiac catheterization. Although oxygen inhalation, oral Bosentan and predonisolone treatment were initiated for the PH and hypereosinophilia, severe PH persisted and she died of PH crisis at the age of 5 months. Deletion of the NEMO gene was identified, and she was genetically diagnosed as IP. The postmortem histo-pathological findings of PA demonstrated grade IV of Heath-Edwards’ grading system. Neither apparent structural cardiac abnormalities, nor infiltration of eosinophil into lung was detected. [Discussion and Conclusion] The histo-pathological findings confirmed her diagnosis of pulmonary arterial hypertension (PAH), suggesting that diffuse microangiopathy might be involved in IP. The modulation of NF-kappaB signaling or hypereosinophilia may be important factor for the development of PAH in IP. Further examination is necessary to determine the mechanism responsible for PAH in IP.