Abstract Background Milk tooth extraction is harmful traditional practices performed by traditional healers without anaesthesia & unsterile materials. The acute and chronic complication of this practice greatly affects the health of children. In order to develop appropriate and effective preventive measures towards such harmful health practice, the extent of the problem and factors facilitating the harmful practice should be investigated. Objective This study was aimed at assessing milk teeth extraction practices and associated factors among mothers had under 5 children in South Achefer district from August 15 to October 15, 2018, North West Ethiopia. Method: A community based cross-sectional study was conducted among 501 mothers having under five children in South Achefer district. A stratified sampling technique method was used to select kebeles and the participants were selected by systematic sampling. Data were collected using a pretested interviewed administered structured questionnaire. Data were checked, coded and entered in to Epi Info 3.5.3 and exported to SPSS (Statistical Package for Social science) version 23 for analysis. Bivariate and multivariable logistic regression was used to identify factors associated with milk teeth extraction practices. The levels of significance was determined using odds ratio with 95% CI and P value <0.05. The results were presented using tables, figures and text as needed. Results: A total of 501 mothers were participated in the study with a response rate of 96.3%. The majority (85.4%) mothers were living in rural. Over half (57.1%) of the children were males and their mean age was 24.0 4±13.45 SD months. The prevalence of milk teeth extraction practice was 31.7%. Residence AOR=3.458(1.350, 8.857), information on solutions of teething symptoms AOR=2.909(1.763, 4.800), peer pressure AOR=7073(4.094, 12.220) and MTE practice is a tradition in the community AOR=3.931(2.112, 7.316) were found to be significant predictors for milk teeth extraction practice. Conclusions and recommendations: Milk teeth extraction practice on <5 children is a public health problem in South Achefer district. Residence, information on solutions of teething symptoms, peer pressure and MTE practice in the community showed significant association with prevalence of milk teeth extraction practice on <5 children.