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Abstract Background Despite the decline in the rate of stunting in Ethiopia, the prevalence is still high and needs immense efforts to achieve the target set to reduce the prevalence. It varies between localities due to individual level factors and dominant livelihood practice in the community. Thus, the aim of this study was to determine the prevalence of stunting and identify factors associated with it in Sodo Zuria district in South Ethiopia. Methods A community based cross sectional study was conducted among 342 children aged 6–59 months paired with mothers/caretakers. Households were selected using systematic sampling. Structured questionnaire was used and mothers/caregivers were interviewed face to face. Standardized anthropometric measurements were used to measure length, and weight and height of a child. Data were entered into Epi Info software version 3.5.1 and exported to SPSS version 20 for analysis. Height for age Z score data were analyzed using WHO Anthro software. Multivariate logistic regression analysis was conducted to identify predictor variables. Statistical significance was considered at p 1500, and children who received pre-lacteal feeding (AOR = 3.8; 95% CI: 1.2–12.2) became predictors for stunting. Conclusion Significant proportion of stunting was found where one third of them were severely stunted. Being female, children aged 12–23 months, using family planning, children with diarrheal morbidity, income and pre-lacteal feeding became predictors for stunting. So Gender-based policies should be enacted in child feeding practice, interventions should focus on the utilization of family planning and appropriate child caring and feeding practices. Water, sanitation and hygiene interventions need to be strengthened.