A genus of unicellular fungi, Pneumocystis (Figure) was likely originally described by Carlos Chagas in 1909 in guinea pigs, although he confused it with a trypanosome and placed it in a new genus, Schizotrypanum. In 1912, Delanoë and Delanoë at the Pasteur Institute published the first description of the new organism as unrelated to trypanosomes and proposed the species name P. carinii in honor of Antonio Carini.

Human Pneumocystis infections were first reported in 1942 by van der Meer and Brug, but not until 1976 did Frenkel report different morphologic and physiologic characteristics of human and rat Pneumocystis isolates. He proposed the name P. jirovecii in honor of Czech parasitologist Otto Jírovec, who reported Pneumocystis as a cause of interstitial pneumonia in infants, although this name change was not accepted by researchers at the time. When Pneumocystis was reclassified from a protozoan to a fungus, the naming convention shifted from the International Code of Zoological Nomenclature to the International Code of Botanical Nomenclature, and the species epithet was modified from jiroveci to jirovecii.