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Introduction Health issues regarding autoimmune diseases in men have been neglected. We here investigated temporal trends in burden of autoimmune diseases in men and assessed inequities in healthcare access and quality worldwide.Methods This ecological, descriptive time-series analysis using Global Burden of Disease estimates included men with autoimmune diseases at all ages covering 204 countries and territories from 1990 to 2021. Age-standardised rates of incidence, prevalence, mortality, disability-adjusted life-years (DALYs), years lived with disability (YLDs) and years of life lost (YLLs) and average annual percentage change were calculated. Global trends were stratified by age, sociodemographic index (SDI), region and country. Overall Quality of Care Index (QCI) and three selected age groups including young (aged 0–14 years), working (aged 15–64 years) and postworking (aged 65+ years) QCI were calculated globally, regionally and nationally.Results Globally, the burden of autoimmune diseases in men significantly decreased from 1990 to 2021. However, in high SDI countries, age-standardised incidence rate increased from 2005, and age-standardised prevalence and YLDs rates increased from 2015. In 2021, significant disparities in QCI scores persisted across SDI levels, with the overall QCI ranging from 74.97 in low–middle countries to 90.55 in high SDI countries. Remarkable ranges in QCI scores between low SDI countries and high SDI countries for the young, working and postworking groups were also detected, with estimates of 82.94 to 92.18, 74.76 to 89.59 and 68.18 to 85.78, respectively. Absolute convergence in QCI was estimated in all these three age groups, with the most prominent convergence in the young group.Conclusions Progress towards controlling autoimmune diseases in men varied widely, with substantially high mortality in low and low–middle SDI countries. Significant inequities in healthcare access and quality persisted across sociodemographic development levels and age groups. Healthcare systems need to improve healthcare access and quality for working and postworking populations while simultaneously maintaining performance among young individuals.