The Naganishia species is a mycosis, previously classified as a non‐neoformans Cryptococcus species. The increased number of naganishial infections occurs predominantly in immunocompromised conditions, especially in people living with HIV with low CD4 cell count, primary immunodeficiencies, and iatrogenic immunosuppression. The lungs can serve as the primary site of infection, leading to various pulmonary manifestations. However, naganishial pleural effusions are unrecognized and challenged in diagnosis because of their presentation, which can mimic tuberculous pleural effusion. Herein, we report the case of a 53‐year‐old man who had undergone kidney transplantation for more than 2 years and presented with chest tightness and dyspnea. Computed chest tomography demonstrated left pleural nodules and pleural effusion, later confirmed as exudative pleural effusion with a lymphocyte predominance. Pleuroscopy revealed multiple small pleural nodules, and biopsies of these nodules were performed. Naganishia spp. was identified by the 18S rRNA sequencing technique.