Stunting is a measure of health inequalities between children with implications that extend into adulthood. Sudan is one of 14 countries carrying 80% of the global burden of stunting. Stunting is reversible if addressed in the first 1000 days of life, so it is essential to identify associated factors in order to target them through government policy. This study aimed to identify factors associated with stunting in children under 5 in Sudan. A secondary analysis of the Sudan Household Health Survey 2010 was done following the UNICEF framework for child under-nutrition which identifies immediate, underlying, and basic factors. We used the chi-square test and multiple regression to adjust for potential confounders. We found that 33.4% (n = 3734) of the children in our study were stunted. Stunting was more common among males, children living in rural areas, born to or household heads with no education, living in households without toilets and had suffered from diarrhea in the past two weeks. Poverty, rurality, poor education and poor sanitation are reversible socioeconomic factors significantly associated with childhood stunting. Government policies aiming to promote child health in Sudan should include poverty-reduction strategies, proper housing, rural development and improving girls’ and women’s education.