BackgroundAssessing disparities in injury is crucial for injury prevention and for evaluating injury prevention strategies, but efforts have been hampered by missing data. This study aimed to show the utility and reliability of the injury surveillance system as a trustworthy resource for examining disparities by generating multiple imputed companion datasets.MethodsWe employed data from the National Electronic Injury Surveillance System-All Injury Program (NEISS-AIP) for the period 2014–2018. A comprehensive simulation study was conducted to identify the appropriate strategy for addressing missing data limitations in NEISS-AIP. To evaluate the imputation performance more quantitatively, a new method based on Brier Skill Score (BSS) was developed to assess the accuracy of predictions by different approaches. We selected the multiple imputations by fully conditional specification (FCS MI) to generate the imputed companion data to NEISS-AIP 2014–2018. We further assessed health disparities systematically in nonfatal assault injuries treated in U.S. hospital emergency departments (EDs) by race and ethnicity, location of injury and sex.ResultsWe found for the first time that significantly higher age-adjusted nonfatal assault injury rates for ED visits per 100,000 population occurred among non-Hispanic Black persons (1306.8, 95% Confidence Interval [CI]: 660.1 – 1953.5), in public settings (286.3, 95% CI: 183.2 – 389.4) and for males (603.5, 95% CI: 409.4 – 797.5). We also observed similar trends in age-adjusted rates (AARs) by different subgroups for non-Hispanic Black persons, injuries occurring in public settings, and for males: AARs of nonfatal assault injury increased significantly from 2014 through 2017, then declined significantly in 2018.ConclusionsNonfatal assault injury imposes significant health care costs and productivity losses for millions of people each year. This study is the first to specifically look at health disparities in nonfatal assault injuries using multiply imputed companion data. Understanding how disparities differ by various groups may lead to the development of more effective initiatives to prevent such injury.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12939-023-01940-4.