The aim of this study was to report the prevalence of self-reported non-communicable diseases among ethnic minority populations in Vietnam and related factors. A total of 5033 individuals aged 15 years and older who belonged to ethnic minority populations from 12 provinces in Vietnam completed a household survey. The overall prevalence of self-reported non-communicable diseases was 12.4% (95% CI: 11.5%–13.4%). Cardiovascular diseases were the most prevalent, followed by diabetes. Ethnicity was shown to have an independently significant correlation to having any non-communicable diseases. Older people, near-poor and non-poor people had significantly higher odds of having non-communicable diseases as compared to younger and poor people.