Pulmonary coinfection by Pneumocystis jirovecii and Histoplasma capsulatum in patients with human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) is common. However, coinfection by extrapulmonary pneumocystis and disseminated histoplasmosis is not. We report a 33-year-old Colombian male patient with a recent diagnosis of HIV/AIDS infection presented with mild flu-like symptoms, chronic diarrhea, cachexia, pale conjunctiva, oral ulcers, and painful hepatomegaly for about 15 days. Pancytopenia without jaundice was documented. Computed tomography showed ground-glass and micronodular miliary patterns suggestive of P. jirovecii pneumonia, pulmonary involvement due to miliary tuberculosis, or histoplasmosis. Histological samples of bronchoalveolar lavage and laparoscopic liver biopsy revealed structures of P. jirovecii, which are verified by polymerase chain reaction. Histoplasma urine antigen was positive. H. capsulatum infection was confirmed by fungal isolation from blood culture and matrix-assisted laser desorption ionization time of flight mass spectrometry. The patient was treated with clindamycin, oral primaquine, and intravenous amphotericin B plus maintenance therapy with itraconazole, and the clinical response was excellent. This case report highlights that despite effective, highly active antiretroviral therapy (ART), rare instances of extrapulmonary coinfection by P. jirovecii and H. capsulatum can still occur. It is therefore important to have a high suspicion index of extrapulmonary pneumocystosis and initiating treatment to prevent mortality. Factors such as severe immunosuppression (CD4+ T-lymphocyte counts <40/mm³) in patients with undiagnosed HIV, treatment-naïve individuals, those who discontinue ART and the absence of P. jirovecii prophylaxis may increase clinicians' suspicion of extrapulmonary manifestations in HIV-infected patients.