Mortality trends among Indigenous peoples in Brazil remain poorly characterised. An ecological time-series study (2010–2022) was conducted, comparing Indigenous and non-Indigenous populations using nationwide open-access demographic and mortality data. Mortality was stratified by sex, age, and ICD-10 groups, populations were compared using Pearson’s chi-square test (p < 0.05), and trends were evaluated with joinpoint regression (JR) to estimate Average Annual Percentage Changes (AAPCs). Between 2010 and 2022, mortality among Indigenous peoples increased by 82.5% (from 2,927 to 5,343), compared with a 42.3% increase in the non-Indigenous population. Over 40% of deaths among Indigenous peoples occurred outside health facilities in both years, versus fewer than 30% among non-Indigenous populations. Crude mortality rates remained lower in Indigenous peoples (2010: 35.8 versus 55.9; 2022: 43.5 versus 74.8 per 10,000 population). However, age-specific differences were marked: mortality among Indigenous children and adolescents (0–19 years) was 3.3 times higher in 2010 and 3.8 times higher in 2022, while mortality among adults aged ≥40 years was approximately 2.5 times lower in both years compared with non-Indigenous populations (all p < 0.05). Mortality rates among Indigenous peoples were consistently higher for maternal, perinatal, and congenital conditions in both 2010 and 2022. JR revealed heterogeneous proportional mortality trends: significant increases in perinatal, congenital, and external causes (AAPC approximately 5.0–6.4%), as well as neoplasms, circulatory, haematological, digestive, respiratory, and endocrine/metabolic diseases (AAPC approximately 1.6–4.4%); a significant decline in infectious and parasitic diseases (AAPC −6.6%); and stability in other groups. Indigenous peoples in Brazil continued to face unfavourable mortality, particularly among children, adolescents, and maternal conditions. Many leading causes of death are preventable. Strengthening primary healthcare, expanding prenatal and perinatal services, improving vaccination and mental-health support, and adopting culturally safe, community-driven strategies to address chronic diseases are critical to reducing inequities and preventable deaths.