Concurrent wasting and stunting (WaSt) is a serious form of malnutrition among young children, particularly vulnerable groups affected by the conflict. Understanding the prevalence and risk factors of WaSt among vulnerable children is important to develop effective intervention measures to reduce the burden of WaSt. The present study aimed to identify the prevalence of and risk factors for WaSt among marginalised children aged 6–59 months in Sana’a city, Yemen. A community-based cross-sectional design was conducted on a total sample size of 450 marginalised children aged 6–59 months who lived at home with their mothers. Multivariable logistic regression analysis was performed and the prevalence of WaSt was found to be 10⋅7 %. Children aged 24–59 months were protected from WaSt (adjusted odds ratio (AOR) 0⋅40, 95 % confidence interval (CI) 0⋅21, 0⋅75). A higher prevalence of WaSt was associated with male sex (AOR 2⋅31, 95 % CI 1⋅13, 4⋅71), no history of being breastfed (AOR 3⋅57, 95 % CI 1⋅23, 10⋅39), acute diarrhoea (AOR 2⋅12, 95 % CI 1⋅12, 4⋅02) and family income sources of assistance from others (AOR 2⋅74, 95 % CI 1⋅08, 6⋅93) or salary work (AOR 2⋅22, 95 % CI 1⋅10, 4⋅47). Continued breast- and bottle-feeding were not associated with WaSt in children aged 6–23 months. Mothers’ age, education and work status, family size and drinking water source were not associated with WaSt. Overall, we found that the prevalence of WaSt among marginalised children remained high. Interventions to improve household income, hygienic conditions and child feeding practices are necessary to promote child growth.