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Abstract Objective Contraceptive discontinuation rate is very common in most developing countries, especially removal in the first year of use is common (18–63%), and the majority of these discontinuations are among women who are still in need of contraception. So the objective of this study was assessing early Implanon discontinuation rate and its associated factors in the study area. Institutional based cross sectional study was conducted and systematic random sampling technique was employed to interview the study participants. A binary logistic regression model was used to test association. Result In this study early Implanon discontinuation rate was 38%, 95% CI (32%, 44%). women who attend secondary [AOR: 95% CI 0.35 (0.14, 0.82)] and more than secondary school [AOR: 95% CI 0.23 (0.09, 0.59)] were less likely to remove Implanon early as compared to those illiterate. Mothers who were not counseled [AOR: 95% CI 2.45 (1.05, 5.69)] and those mothers who had a side effect of the method [AOR: 95% CI 2.66 (1.23, 5.72)] discontinue the method early. The study revealed that early Implanon discontinuation rate was high. Women’s educational level, presence of side effect and effective counseling were independent predictors of early Implanon removal.