Objective: This article aims to analyse the evolution of 40 Sustainable Development Goals’ (SDGs) health-related indicators in Brazil and Ecuador from 1990 to 2019. Study design Epidemiological study of long-term trends in 40 SDGs’ health-related indicators for Brazil and Ecuador from 1990 to 2019, using estimates from the Global Burden of Disease Study. Methods: Forty SDGs’ health-related indicators and an index from 1990 to 2017 for Brazil and Ecuador, and their projections up to 2030 were extracted from the Institute for Health Metrics and Evaluation’s Global Burden of Disease website and analysed. The percent annual change (PC) between 1990 and 2019 was calculated for both countries. Results: Both countries have made progress on child stunting (Brazil: PC = −38%; Ecuador: PC = −43%) and child wasting prevalences (Brazil: PC = −42%; Ecuador: PC = −41%), percent of vaccine coverage (Brazil: PC = +215%; Ecuador: PC = +175%), under-5 (Brazil: PC = −75%; Ecuador: PC = −60%) and neonatal mortality rates (Brazil: PC = −69%; Ecuador: PC = −51%), health worker density per 1000 population (Brazil: PC = +153%; Ecuador: PC = +175%), reduction of neglected diseases prevalences (Brazil: PC = −40%; Ecuador: PC = −58%), tuberculosis (Brazil: PC = −27%; Ecuador: PC = −55%) and malaria incidences (Brazil: PC = −97%; Ecuador: PC = −100%), water, sanitation and hygiene mortality rates (Brazil and Ecuador: PC = −89%). However, both countries did not show sufficient improvement in maternal mortality ratio to meet SDGs targets (Brazil: PC = −37%; Ecuador: PC = −40%). Worsening of indicators were found for violence, such as non-intimate partner violence for both countries (Brazil: PC = +26%; Ecuador: PC = +18%) and suicide mortality rate for Ecuador (PC = +66%), child overweight indicator for Brazil (PC = −67%), disaster mortality rates (Brazil: PC = +100%; Ecuador: PC = +325%) and alcohol consumption (Brazil: PC = +46%; Ecuador: PC = +35%). Conclusions: Significant improvements are necessary in both countries requiring the strengthening of health and other policies, particularly concerning the prevention and management of violence and alcohol consumption, and preparedness for dealing with environmental disasters.