Fungal superinfections have been reported in patients with coronavirus disease 2019 (COVID-19). We analyzed the incidence and clinical characteristics ofPneumocystis jiroveciipneumonia (PCP) in non-human immunodeficiency virus patients at a tertiary hospital between 2016 and 2022 to evaluate the impact of the COVID-19 pandemic on PCP. The study period was divided into pre-COVID-19 and COVID-19 eras based on the pandemic declaration by the World Health Organization. Among the 113 patients included, the incidence of PCP in the COVID-19 era (37/1000 patient-years) was significantly higher than that in the pre-COVID-19 era (13.1/1000 patient-years) (p< 0.001). Co-infection with invasive pulmonary aspergillosis (IPA) also increased (2.4% vs. 18.3%,p= 0.013). Independent risk factors for PCP-related mortality were previous glucocorticoid use, hypoxemia, acute kidney injury, and IPA co-infection. Risk factors for IPA in patients with PCP included previous use of tyrosine kinase inhibitors, COVID-19 infection within 30 days, leukopenia, and intensive care unit admission. In the COVID-19 era, 12 (16.9%) patients with PCP had a history of COVID-19 infection within 90 days; however, infection was not associated with mortality. Active evaluation of patients with suspected PCP and assessment of IPA co-infection risk may help improve the outcomes of patients with PCP.