Pneumocystis jiroveci (P. jiroveci) pneumonia is known as a common opportunistic infection in patients with impaired immunity. Underlying disease or conditions related to the development of P. jiroveci pneumonia include acquired immunodeficiency syndromes, as well as malignancies and congenital immune deficiency disorders. We describe a 5-month-old boy without significant medical history who was admitted at our hospital because of fever, tachypnea, vomiting, diarrhea, and lethargy whose condition became worse within several hours after admission. A chest X-ray showed bilateral diffuse infiltration and high resolution computed tomography showed diffuse bilateral ground-glass opacity. The patient was diagnosed with P. jiroveci pneumonia by direct immunofluorescent antibody staining from lung biopsy and he was later diagnosed with agammaglobulinemia. Although the boy was treated with antibiotics, high-dose corticosteroids and mechanical ventilation, he expired on the 5th hospital day. Here, we report the case of P. jiroveci pneumonia in a boy with agammaglobulinemia.