Saprochaete capitata may cause uncommon severe infections, especially in immunocompromised patients. Here, we describe a rare case of urinary tract infection by S. capitata in a chronic kidney disease and diabetes mellitus patient, which occur during anidulafungin therapy. Mycological examinations of urine were positive to S. capitata identified by mass spectrometry and confirmed by ITS sequencing. Minimum inhibitory concentration (MIC) of the isolate for amphotericin B, fluconazole, itraconazole, voriconazole and, anidulafungin were 2, 16, 1, 1, and 8μg/mL, respectively. Presence of S. capitata infection was not known. Clinicians should be aware about these rare opportunistic fungal pathogens, particularly those with intrinsic or variable resistance to antifungals including echinocandins.