This commentary provides a critical analysis of the integration of traditional medicine into Uganda’s formal healthcare system, focusing on the period from 2021. It argues that prevailing policy frameworks exhibit a significant gendered oversight, undermining equitable integration. Employing a qualitative document analysis methodology, this study systematically examines key policy documents, including the 2021 National Policy on Traditional and Complementary Medicine. This is complemented by a review of selected contemporary case studies and institutional reports to triangulate findings. The analysis reveals that, despite legislative progress, implementation remains fragmented and fails to address the gendered dynamics of practice. It foregrounds the central, yet often unrecognised, role of women as custodians and practitioners of indigenous knowledge, demonstrating how their expertise is systematically sidelined. Consequently, the specific health needs of the women and girls they predominantly serve are neglected. This oversight perpetuates a systemic undervaluation of women’s epistemic contributions within the health sector. The commentary concludes by advocating for a more equitable, gender-sensitive integration model. For Uganda’s health governance, this necessitates moving beyond tokenistic inclusion to foster collaborative partnerships that validate traditional medical knowledge as a vital component of a decolonised, accessible, and culturally resonant healthcare system.