Undernutrition is a major global health problem. Various types of animal milk are used for feeding children at early ages; however, associations of camel milk (CaM) and bovine milk (BM) with the nutritional status of children have not been explored. A comparative community-based cross-sectional study was conducted among pre-schoolers in rural pastoral districts of Somali, Ethiopia. Children were selected from households with lactating camels or cows. Anthropometric measurements followed standard procedures for height-for-age, weight-for-age and weight-for-height scores. Independent sample t-tests identified significant differences in anthropometric indices based on the type of milk consumed. Multivariable logistic regression was used to examine associations between milk consumption and other predictors of growth failures. The prevalence of stunting was 24⋅1 % [95 % confidence interval (CI) 20⋅5, 28⋅3] of pre-schoolers, 34⋅8 % (95 % CI 29⋅9, 39⋅6) were wasted and 34⋅7 % (95 % CI 30⋅1, 39⋅9) were underweight. Higher proportions of BM-fed children were severely stunted, wasted and underweight compared with CaM consumers. Using logistic regression models, children who consumed BM [adjusted odds ratio (AOR): 2⋅10; 95 % CI 1⋅22, 3⋅61] and who were anaemic (AOR: 4⋅22; 95 % CI 2⋅23, 7⋅98) were more likely to be stunted than their counterparts, while girls were less likely to be stunted than boys (AOR: 0⋅57; 95 % CI 0⋅34, 0⋅94). Similarly, children who consumed BM (AOR: 1⋅97; 95 % CI 1⋅20, 3⋅24), who were anaemic (AOR: 2⋅27; 95 % CI 1⋅38, 3⋅72) and who drank unsafe water (AOR: 1⋅91; 95 % CI 1⋅19, 3⋅07) were more likely to be underweight than their counterparts. In conclusion, CaM consumption was associated with lower prevalence of stunting and underweight than BM. Promoting CaM in pastoralist areas may help to curb the high level of undernutrition.