We report a case of superinfection of liver cysts caused by Candida albicans and Staphylococcus lugdunensis in a patient with autosomal dominant polycystic kidney disease. A 69-year-old man with chief complaints of headache and blurred vision was admitted to the former institution for the evaluation of suspected temporal arteritis. He was prescribed oral prednisolone (55 mg/day) as a preemptive treatment; however, he became febrile and presented with bilateral flank pain during prednisolone tapering. Blood culture revealed fungemia as a result of Candida famata infection; thus, micafungin treatment was started. Thereafter, recrudescence of the C-reactive protein level ensued. Then a cyst infection as visualized on magnetic resonance imaging led to cyst aspiration sclerotherapy. Cyst aspirate culture revealed the presence of C. albicans in one of the cysts and S. lugdunensis in two of the cysts. The patient was clinically stabilized with an additional 3 weeks of antibiotic and antifungal drug administration.