Transplant-associated thrombotic microangiopathy (TA-TMA) is an under-recognized yet potentially devastating complication of hematopoietic stem cell transplantation which had increased awareness in recent years. This report summarizes territory-wide experience of paediatric TA-TMA in the Hong Kong Children’s Hospital from 1 April 2019 to 31 March 2021. Total six patients were identified among 73 transplants performed. Median duration of onset was 2.5 months post-HSCT. Three patients died while all 3 survivors suffered from stage 2 to 5 chronic kidney disease despite administration of eculizumab. To conclude, recognition and diagnosis of TA-TMA is challenging. Clinical utility of complement blockage with eculizumab is limited.