The transition from nomadism to sedentary lifestyle has introduced changes in diets and undernutrition is endemic among settled pastoral households. This study aimed to investigate the underlying factors affecting stunting, underweight, and wasting of children aged 6–59 months in Marsabit County, Kenya. A cross‐sectional household survey was conducted in six wards capturing pastoral, agro‐pastoral, and urban livelihood practices. Using multistage sampling method, 394 children aged 6–59 months participated with written consent from the caregivers. A pretested questionnaire and anthropometric measures were used during data collection. Population characteristics were summarized into means and proportions, while chi‐square and analysis of variance were used to evaluate associations between variables. Backward logistic regressions were used to explore predictors of stunting, underweight, and wasting, respectively. The results showed that the mean Height for Age Z‐score, Weight for Age Z‐score, and Weight for Height Z‐score were −1.51, 1.54, and 1.02, respectively. The prevalence of stunting, underweight, and wasting was 38.1%, 23.0%, and 18.5%, respectively. The age of child, source of drinking water, and waste disposal were some of the main factors influencing stunting among children. In conclusion, the prevalence of undernutrition was high compared to the World Health Organization recommended cutoffs. Water sources hygiene, and caregiver's income were some of the main predictors of undernutrition among children. Development agencies need to focus on the supply of potable water, access to toilet facilities, in addition to nutrition education on hygienic complementary feeding practices among pastoral caregivers.