Fungal peritonitis is a serious complication of chronic peritoneal dialysis (CPD) and is frequently associated with CPD drop-out. Paecilomyces variotii, a common saprophytic fungus, rarely causes human infection. To date, only nine adult or adolescent patients with P. variotii peritonitis during continuous ambulatory peritoneal dialysis have been reported. In all patients, successful treatment required antifungal therapy and removal of the peritoneal catheter. We report the first case of P. variotii peritonitis in an infant on automated peritoneal dialysis successfully treated with combined intraperitoneal and oral fluconazole, without removal of the peritoneal catheter.