Background Leaving no one behind has been an important marker of the Sustainable Development Goals. Closing the gap in malnutrition between children of different backgrounds aligns well with the tenet of this international agenda. To this end, high-quality evidence of the magnitude and trends of socioeconomic and geographic related existing inequalities in the childhood stunting among Sudanese children emanate from this study help for policy maker and planners to design and implement effective interventions to narrow down inequality. Methods We used the World Health Organization’s (WHO) Health Equity Assessment Toolkit (HEAT) for our analysis of stunting inequality. Following standard equity analysis methods recommended by the WHO, we performed the disaggregated analysis of stunting across five equity stratifiers: Wealth, education, residence, sex, and sub-national regions. Then, we summarized stunting inequality through four measures of inequality: Difference, Ratio, Slope Index of Inequality (SII), and Relative Index of Inequality (RII). The point estimates of stunting were accompanied by 95% confidence intervals to measure the statistical significance of the findings. Results In this study, the national average childhood stunting prevalence was increased by 4% from 2010 to 2014. The findings revealed stark inequalities in stunting in all the studied dimensions of inequality. Huge inequality has existed along the wealth quintiles. Simple difference measure for education was increased by four points and simple relative measure decreased by one point for economic status. Conclusions Sex, residence and, geographically related inequalities remain unchanged over time, while economic status and educational inequality had seen a change by some inequality measures over the same time period.