This dataset derives from the research project “Resilience of Indigenous Peoples’ Healthcare system”, led by Sandrine Gallois, funded by the Beatriu de Pinós Programme and the Ministry of Research and Universities of the Government of Catalonia (BP2020-00216). This research explores the local medical system of the Baka people, forager-horticulturalists living in southeastern Cameroon. Specifically, it aims to assess the adaptive capacity of their medical system to the current social-ecological changes, by taking an interdisciplinary lens, diving into the local ecological knowledge and practices of the Baka and the different disturbances affecting their health and healthcare system. This dataset is part of this broad research, focusing specifically on Baka children’ knowledge regarding medicinal plants. The data were collected in two villages from southeastern Cameroon, in the Lomié and Messok districts, in 2022, reaching a total of 106 children, from 6 to 16 years-old (46 boys and 60 girls). The dataset compiles the local names of medicinal plants reported by the children from three methods used: the freelising interviews, the walk-in-the-wood trips and the individual knowledge surveys.