The overexpression of pyruvate dehydrogenase kinase 1 (PDK1) has been observed in a number of different cancers, making it a potential target for the treatment of cancer. In this study, we used bioinformatics methods to analyse the immunophenotype of osteosarcoma (OS) and identified PDK1 as a critical factor in the different immune states of the disease. A pan-cancer analysis revealed a robust correlation between PDK1 and the tumour microenvironment. Moreover, our findings corroborate the overexpression of PDK1 in OS, whereby it facilitates tumour development via the NF-κB pathway. From a mechanistic perspective, PDK1 has the capacity to bind and phosphorylate USP5. The phosphorylation of USP5 by PDK1 activates its deubiquitinating activity, leading to the stabilisation of IKKγ protein and subsequent activation of the NF-κB signalling pathway, which ultimately promotes the growth of OS cells. Molecular simulation docking, pull-down assays, and SIP experiments were employed to further identify arctigenin (ATG) as a small molecule inhibitor of PDK1. The findings demonstrated that ATG effectively inhibited the growth of OS cells and tumour xenograft models. Collectively, these results highlight that PDK1 influences NF-κB in OS through the PDK1-USP5-IKKγ axis. Furthermore, the identification of ATG as an effective inhibitor of PDK1 suggests that ATG may serve as a promising lead compound for the treatment of OS.