Kaposiform haemangioendothelioma (KHE) research faces challenges due to the lack of established cell lines and suitable animal models. Our study aimed to establish KHE cell lines, spheroids and refine murine models to mimic disease characteristics, advancing our understanding of KHE pathogenesis and exploring novel therapies. Primary KHE cells were sorted using CD31 antibodies and cultured into spheroids. These cells were then injected into mice, and the resulting tumours were analysed using immunohistochemistry. Preliminary exploration of the potential mechanisms of sirolimus action on KHE was conducted through transcriptome sequencing. CD31+ KHE cells were isolated and characterised from three out of six patients. The CD31+ KHE cells demonstrated positive expression of essential markers such as CD31, Ki67 and LYVE1, consistent with the profiles observed in KHE tumours. Additionally, subcutaneous tumours displayed similar positive expression of key markers, reminiscent of KHE tumours. Transcriptome sequencing revealed downregulation of ATG9B after sirolimus treatment in CD31+ KHE cells. CD31+ KHE cells can replicate human KHE in murine models, offering a valuable tool for studying pathogenesis. Our findings also suggest a potential mechanism of sirolimus action in treating KHE, warranting further investigation into novel therapeutic strategies.© 2025 The Author(s). Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.