This study described infection-related supportive care practices amongst centres participating in two large paediatric acute myeloid leukaemia (AML) cooperative groups, Children’s Oncology Group (COG) and Berlin-Frankfurt-Muenster (BFM). We surveyed 216 COG and 55 BFM institutions. The overall survey response rate was 83·8%. Antibacterial prophylaxis was more common among BFM (15/46, 32·6%) compared to COG (24/180, 13·3%, P < 0·0001) institutions. Antifungal prophylaxis also was more common among BFM (42/46, 91·3%) compared to COG (137/178, 77·0%, P = 0·03). There were systematic differences in infection-related supportive care practices. This information may be used to encourage harmonization of supportive care practices and future randomized trials.