Background: Malnutrition is a global problem that affects schoolchildren and can increase the risk of diseases in adulthood. Adult members of the Yaqui Indigenous group have been shown to have serious health problems, and Yaqui schoolchildren could therefore find themselves in a similar situation. Objective: To evaluate the nutritional status, lipid profile and associated factors in a sample of Yaqui schoolchildren. Material and methods: A total of 109 Yaqui schoolchildren who lived in their localities of origin were recruited. Anthropometric measurements were carried out, a venous blood sample was extracted in fasting conditions, and several questionnaires were applied. Results: The prevalence of overweight/obesity was 38.5%, with no cases of chronic malnutrition being recorded; 38.6% of the children had dyslipidemia. Fiber consumption was a protective factor against overweight/ obesity, while fat intake was a risk factor. The physical activity score was found to be a protective factor against dyslipidemia, and the risk factors were BMI-for-age Z-scores, waist circumference, family history of dyslipidemia, educational level, and permanent employment. Conclusions: Yaqui schoolchildren equally suffer from a high proportion of overweight/obesity and dyslipidemia. The associated factors may be useful for the design of contextualized interventions for this population.