Background China and India jointly account for 38% of the world population, so understanding the burden attributed to mental, neurological, and substance use disorders within these two countries is essential. As part of the Lancet/Lancet Psychiatry China-India Mental Health Alliance Series, we aim to provide estimates of the burden of mental, neurological, and substance use disorders for China and India from the Global Burden of Disease Study 2013 (GBD 2013). Methods In this systematic analysis for community representative epidemiological studies, we conducted systematic reviews in line with PRISMA guidelines for community representative epidemiological studies. We extracted estimates of prevalence, incidence, remission and duration, and mortality along with associated uncertainty intervals from GBD 2013. Using these data as primary inputs, DisMod-MR 2.0, a Bayesian meta-regression instrument, used a log rate and incidence-prevalence-mortality mathematical model to develop internally consistent epidemiological models. Disability-adjusted life-year (DALY) changes between 1990 and 2013 were decomposed to quantify change attributable to population growth and ageing. We projected DALYs from 2013 to 2025 for mental, neurological, and substance use disorders using United Nations population data. Findings Around a third of global DALYs attributable to mental, neurological, and substance use disorders were found in China and India (66 million DALYs), a number greater than all developed countries combined (50 million DALYs). Disease burden profiles differed; India showed similarities with other developing countries (around 50% of DALYs attributable to non-communicable disease), whereas China more closely resembled developed countries (around 80% of DALYs attributable to non-communicable disease). The overall population growth in India explains a greater proportion of the increase in mental, neurological, and substance use disorder burden from 1990 to 2013 (44%) than in China (20%). The burden of mental, neurological, and substance use disorders is estimated to increase by 10% in China and 23% in India between 2013 and 2025. Interpretation The current and projected burden of mental, neurological, and substance use disorders in China and India warrants the urgent prioritisation of programmes focused on targeted prevention, early identification, and effective treatment.