Nepal harbors many ethnomedicinal plants distributed throughout the country’s diverse geography. It is crucial to document plants’ ethnobotanical knowledge for further research and conservation. This study aimed to conduct a quantitative ethnobotanical analysis of the medicinal plants used in the Varagung Muktichhetra Rural Municipality of Mustang District, Nepal. Data were collected through a household survey (N = 101), using snowball sampling with 40% sampling intensity, 12 Key Informant Interviews (KIIs), and two Focus Group Discussions (FGDs). The data was analyzed using different quantitative tools: Informant consensus factor (Fic), Fidelity Level (FL), and Use Values (UV). A total of 54 medicinal plants belonging to 32 families were documented, which were used to treat 40 different ailments. The family Asteraceae represented the maximum number of plants being used. Herbs were most frequently used (59%), and root (n =10) was the most used plant part. Neopicrorhiza scrophulariiflora was the most frequently used and preferred species (FL = 65% and UV = 0.62). Fever (Fic = 0.88) and gastrointestinal disorder (Fic = 0.86) were the major ailment categories treated. Oral (76%) was the main route of administration of medicines in the body, and the most used form of medicine preparation was paste (46%). Unsustainable harvesting, illegal collection, and forest fire were the major threats to medicinal plants and were highly significant after applying the non-parametric Friedman test. Enactment of a policy that focuses on conservation, sustainable harvesting, and domestication of highly valued medicinal plants is recommended to policymakers.