Advances in the treatment and prevention of Pneumocystis jirovecii infection (PJI) in human immunodeficiency virus (HIV) patients decreased incidence and mortality dramatically, however, it may be associated with an increased frequency of unusual manifestation such as cystic formation, pneumothorax, focal infiltration, nodular formation, or extrapulmonary lesions. We report three cases of PJI with atypical manifestations. Each case demonstrates different clinical features: multiple nodular pulmonary lesion (32-year-old man with abnormal chest X-ray finding), subpleural mass-like lesion (43-year-old man with left visual loss and right pleuritic chest pain), and extrapulmonary mass-like lesions in the liver, lymph nodes, and small bowel (39-year-old man with cough, sputum, and dyspnea). P. jirovecii was confirmed in all 3 cases and they were treated well. It is necessary to understand that PJI shows variable clinical features.