• Pharmacokinetics of intravenous fluconazole and ganciclovir were measured in a patient receiving extracorporeal membrane oxygenation therapy (ECMO). • The patient had been newly diagnosed with human immunodeficiency virus/acquired immunodeficiency syndrome, and required fluconazole prophylaxis and ganciclovir therapy for cytomegalovirus infection. • Pre-oxygenator, post-oxygenator and peripheral arterial samples were taken. • Intravenous fluconazole 6 mg/kg (24-h) is adequate for prophylaxis and intravenous ganciclovir 5 mg/kg (12-h) is adequate for therapy in patients on ECMO. Extracorporeal membrane oxygenation (ECMO) can affect antimicrobial pharmacokinetics. This case report describes a 33-year-old male with newly diagnosed acquired immunodeficiency syndrome presenting in acute severe type 1 respiratory failure. On investigation, the patient had positive cultures for Candida albicans from respiratory specimens and high blood cytomegalovirus titres, and required venovenous ECMO therapy for refractory respiratory failure. Intravenous fluconazole (6 mg/kg, 24-h) and ganciclovir (5 mg/kg, 12-h) was commenced. Pre-oxygenator, post-oxygenator and arterial blood samples were collected after antibiotic administration, and were analysed for total fluconazole and ganciclovir concentrations. Although there was a 40% increase in the volume of distribution for fluconazole relative to healthy volunteers, the pharmacodynamic targets for prophylaxis were still met. The area under the curve exposure of ganciclovir (50.78 mg•h/L) achieved target thresholds. The ECMO circuit had no appreciable effect on achievement of therapeutic exposures of fluconazole and ganciclovir. [ABSTRACT FROM AUTHOR]