Chronic granulomatous disease (CGD) is a congenital immunodeficiency, characterised by significant infections due to an inability of phagocyte to kill catalase-positive organisms including certain fungi such as Aspergillus spp. Nevertheless, other more rare fungi can cause significant diseases. This report is a systematic review of all published cases of non-Aspergillus fungal infections in CGD patients. Analysis of 68 cases of non-Aspergillus fungal infections in 65 CGD patients (10 females) published in the English literature. The median age of CGD patients was 15.2 years (range 0.1–69), 60% of whom had the X-linked recessive defect. The most prevalent non-Aspergillus fungal infections were associated with Rhizopus spp. and Trichosporon spp. found in nine cases each (13.2%). The most commonly affected organs were the lungs in 69.9%. In 63.2% of cases first line antifungal treatment was monotherapy, with amphotericin B formulations being the most frequently used antifungal agents in 45.6% of cases. The overall mortality rate was 26.2%. Clinicians should take into account the occurrence of non-Aspergillus infections in this patient group, as well as the possibility of a changing epidemiology in fungal pathogens. Better awareness and knowledge of these pathogens can optimise antifungal treatment and improve outcome in CGD patients.