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Background In Ethiopia, inappropriate feeding including prelacteal feeding is one of the immediate causes of undernutrition. The objective of this study was to assess the magnitude and associated factors of prelacteal feeding practices among mothers of children aged less than one year in Rural Pastoralist Communities of Afar, Ethiopia. Methods A cross-sectional study was conducted in the Afar Region, Ethiopia from May to June 2016. A total of 424 mothers were included in the study. A two-stage cluster sampling technique was used to select sample clusters and households. A pre-tested and structured questionnaire was used as a data collection instrument. SPSS version 25 was used to analyze the data. Model goodness of fitness was assessed using Hosmer and Lemeshow test. Multi-collinearity between independent variables was checked. Binary logistic regression analysis was used to identify the association between the explanatory variables and prelacteal feeding practices. Multivariable logistic regression was also used to determine the independent predictors of prelacteal feeding practices. Result In this study, 75.7% (95% CI 71.1%, 79.7%) of mothers gave prelacteal feeds to their newborns. The odd of prelacteal feeding was 2.32 times higher in mothers whose husbands didn’t attend formal education as compared to their counterpart (AOR = 2.32, 95% CI: 1.18-4.5). The odds of prelacteal feeding was 7 times higher for infants delivered at home compared to infants delivered at a health facility (AOR = 7.52, 95% CI:3.44, 16.45). Fail to have skin to skin contact between the mother and the newborn increases the odds of prelacteal feeding by 5 times than their counterparts (AOR=5.12, 95%CI: 2.14, 12.21). Conclusion Three-fourth of the children in Rural Pastoralist Communities of Afar received prelacteal feeding. Home delivery, husband education and skin to skin contact immediately after birth were found to be independent predictors of prelacteal feeding in the pastoralist communities. Strengthening the behavior change communication on optimal infant and young child feeding, promotion of husband education and institutional delivery and skin to skin contact immediately after birth are the recommendations.