Nutritional status of children is an important outcome measure of their health status. However, nutritional status and associated factors of pastoralist children were not well documented in Benna Tsemay Woreda, South Omo Zone, Southern Ethiopia. Therefore, this study was designed to assess nutritional status and associated factors among pastoralist children aged 6-23 months in Benna Tsemay Woreda, South Omo Zone, Southern Ethiopia. A community-based cross sectional study was conducted among 645 pastoralist children aged 6-23 months from February-March 2016. A stratified random sampling technique was used to select kebeles (smallest administrative unit) and children. Out of thirty-two kebeles, six were randomly selected. Data were collected using a structured questionnaire, 24 hour food recall and anthropometric measurements. Quantitative data were collected and analyzed using SPSS for windows version 20.0. Anthropometric indices were computed using WHO Anthro 2011 software (version 3.2.2). Bivariate and multivariable logistic regression analyses were conducted. Crude odds ratio (COR) and adjusted odds ratio (AOR) with 95% confidence interval (CI) were reported. Prevalence of stunting and underweight were higher in fewer than two children in Benna Tsemay compared to the national average. This study showed, being older child (12-23 months) (AOR=3.29, 95%CI, 2.03-5.32), being from agro-pastoralist (AOR=0.46, 95%CI, 0.24-0.88), middle wealth quantile household (AOR=0.40, 95%CI, 0.20-0.77), use of treated water (AOR=0.60, 95%CI, 0.37-0.96), being second birth order (AOR=2.17, 95%CI, 1.11-4.24), being female child (AOR=0.55, 95%CI, 0.37-0.82) and good child feeding practice of mothers (AOR=0.47, 95%CI, 0.28-0.78) were significantly associated with stunting of pastoralist children in Benna Tsemay Woreda (p<0.05). Having large family size (≥6 individuals) (AOR=30.93, 95%CI, 4.91-194.7), polygamous marriage (AOR=2.46, 95%CI, 1.07-5.61), being from agro-pastoralist (AOR=0.19, 95%CI, 0.05-0.66) and farming as maternal occupation (AOR=3.00, 95%CI, 1.36-6.62) were significantly affected with thinness of children (p<0.05). Being from pastoralist (AOR=3.18, 95%CI, 1.74-5.81) and being female child (AOR=0.35, 95%CI, 0.14-0.89) were significantly predicted underweight in children (p<0.05). In conclusion, high numbers of pastoralist children are suffering from chronic malnutrition with low dietary diversity score (DDS). Large numbers of mothers have poor infant and young child feeding (IYCF) practices. Being from pastoralist and poor family, elder and male child, and poor IYCF practices, polygamous marriage, and poor health service are factors for child under nutrition. Therefore, the authors recommend interventions targeting on community-based nutrition education on IYCF, dietary diversity, cultural food taboos, and family planning in Benna Tsemay pastoralist community.