BACKGROUND: There is scarce gender-disaggregated evidence on the burden of disease (BD) worldwide and this is particularly prominent in low- and middle-income countries. The objective of this study is to compare the BD caused by non-communicable diseases (NCDs) and related risk factors by gender in Mexican adults. METHODS: We retrieved disability-adjusted life years (DALYs) estimates for diabetes, cancers and neoplasms, chronic cardiovascular diseases (CVDs), chronic respiratory diseases (CRDs), and chronic kidney disease (CKD) from the Global Burden of Disease (GBD) Study from 1990-2019. Age-standardized death rates were calculated using official mortality microdata from 2000 to 2020. Then, we analysed national health surveys to depict tobacco and alcohol use and physical inactivity from 2000-2018. Women-to-men DALYs and mortality rates and prevalence ratios (WMR) were calculated as a measure of gender gap. FINDINGS: Regarding DALYs, WMR was >1 for diabetes, cancers, and CKD in 1990, indicating a higher burden in women. WMR decreased over time in all NCDs, except for CRDs, which increased to 0.78. However, WMR was <1 for all in 2019. The mortality-WMR was >1 for diabetes and cardiovascular diseases in 2000 and <1 for the rest of the conditions. The WMR decreased in all cases, except for CRDs, which was <1 in 2020. The WMR for tobacco and alcohol use remained under 1. For physical inactivity, it was >1 and increasing. CONCLUSIONS: The gender gap has changed for selected NCDs in favour of women, except for CRDs. Women face a lower BD and are less affected by tobacco and alcohol use but face a higher risk of physical inactivity. Policymakers should consider a gendered approach for designing effective policies to reduce the burden of NCDs and health inequities.