This article analyses the historical development of Mongolian Traditional Medicine (MTM) through Michel Foucault’s “archaeology of knowledge” framework. The era of ancient shamanism constituted a metaphysical epistemic regime in which illness was explained through supernatural forces. A first epistemic rupture emerged in the thirteenth century: from this point until the late fourteenth century, within the Mongol Empire there stand up a multi-centred knowledge space alongside shamanic practices, Tibetan and Chinese medical traditions, as well as elements of Western medicine coexisted. After the fall of the Yuan dynasty, this pluralistic configuration weakened, leading to a resurgence of shamanic discourse that remained dominant until the spread of Tibetan Buddhism. Another rupture occurred in the late sixteenth century, after which, between the seventeenth and twentieth centuries, Tibetan medicine became the principal institutionalised discourse in Mongolia. During this period, a Tibetanised epistemic regime took shape, characterised by Tibetan terminology, diagnostic methods, pharmacological recipes, and the monopolising role of monastic physicians. From the mid-nineteenth century onward, the discourse of European scientific medicine began to layer itself onto this Tibetan framework, marking an important precursor to the next epistemic rupture in the early twentieth century. Under the communist regime, particularly between 1937 and 1990, Mongolian traditional medicine was first suppressed and later reorganised into a government-controlled, “scientifically” systematised institutional form. This was not the annihilation of discourse but rather a reconfiguration of MTM within a new power-knowledge configuration. Since 1990, MTM has existed within a pluralistic, multi-centred discursive environment, encompassing market-based, religious, traditional, and biomedical frameworks, resulting in a fragmented knowledge system. Thus, the historical evolution of Mongolian Traditional Medicine is best understood not as a linear continuum but as a series of layered discourses marked by ruptures, transitions, overlaps, and revivals. Its history is shaped by successive regimes of truth, each producing distinct configurations of medical knowledge.