Cyberlindnera fabianii, an ascomycetous yeast, is a rare human pathogen. Here, we describe the first reported case of central venous (CV) access port-related blood-stream infection caused by C. fabianii. An 80-year-old Asian man presented to our department with a mass in the pancreas. A diagnosis of pancreatic cancer (cT4N0M0, cStage III) was made. A catheter with CV access port was inserted, and anticancer chemotherapy and radiotherapy was initiated. One year after the first visit, he was urgently admitted to our hospital due to recurrent hematemesis. On day 37, organism cultures of the blood and catheter tip were positive for Candida pelliculosa by the BD PHOENIX™ 100 system. On the basis of these findings, CV port-related blood-stream infection caused by C. pelliculosa was diagnosed, and treatment with micafungin (MCFG) was initiated. On day 51, the blood culture converted to negative. On day 65, MCFG was stopped. The cultured strain was sent to reference laboratory where Cyberlindnera fabianii was identified by MALDI-TOF mass spectrometry and direct sequencing of the internally transcribed spacer region. The present case report describes the first known case of CV access port-related blood-stream infection caused by C. fabianii. MCFG was successfully used to treat the fungemia caused by C. fabianii. Although the incidence of uncommon yeast species causing human infections has gradually increased in recent years, conventional biochemical methods may offer limited usefulness for identifying these rare organisms. Accordingly, MALDI-TOF mass spectrometry or molecular assays may be required to identify these uncommon fungal species.