Background: Scarce epidemiological information on stroke in Mexico impedes evidence-based decisions and debilitates the design of effective prevention programmes at the local level. Methods: Ecological and secondary analysis of Global Burden of Disease national and subnational data for Mexico, from 1990 to 2019. We analysed the incidence, prevalence, deaths, premature mortality, disability, and DALYs due to cerebrovascular disease included to identify the differences in the burden of stroke in Mexico by type of stroke (ischaemic [IS], intracerebral haemorrhage [ICH] and subarachnoid haemorrhage [SAH]), sex, age groups, and state levels ordered by quartiles of Sociodemographic Index (SDI). Means and 95% uncertainty intervals are reported. Findings: Reductions in all metrics of total stroke occurred during the 1990 to 2005 period; however, this declining trend was followed up by stagnation of progress from 2006 to 2019, except for premature mortality. This pattern of the declining trend was observed also for IS and to a lesser extent for ICH, while SAH showed no major changes during the 1990-2019 period. The magnitude of decline was higher in females for total stroke for incidence, prevalence and YLDs rates. The less developed states by SDI exhibited the lowest improvements during the period, particularly for ICH metrics. Interpretation: The reduction in stroke burden in Mexico did not follow the same pace for all types of stroke, with regional differences by SDI and by sex. Study findings reveal the need for strengthening prevention policies to address health disparities in the burden of stroke by sex and states, within the fragmented Mexican Healthcare System.