Background Implanon is an effective form of long-acting reversible contraceptive used to prevent conception with a clinical failure rate of less than one per 100 users. However, in sub-Saharan countries the utilization of implanon was very low. Regardless of low utilization; its early discontinuation is very common in most developing countries including Ethiopia. Objectives To assess the prevalence of early implanon discontinuation and associated factors among women ever used implanon in Mettu district. Methods A community based cross-sectional study design was conducted from October 11 to December 4, 2020 G C. A total of 430 women were included in the study by systematic random sampling technique. Data were entered into epi data version 3.1 and analyzed by SPSS version 25.0. Descriptive analysis was computed to describe descriptive results. Logistics regression was computed to see the relative effect of factors on the outcome variable. Adjusted odds ratio was calculated with 95% confidence intervals to show strength of association and p-value < 0.05 was used to declare statistical significance. The finding of the study was presented using narrations, tables and chart. Result The total proportion of early implanon discontinuation among 430 mothers was 19.3%. Women who did not counseled about the presence of alternatives methods [AOR = 2.28: 95% CI (1.22-4.26)], women who experienced dizziness after insertion of implanon [AOR = 1.90: 95% CI (1.06-3.43)] and being having menstrual disturbance after insertion of implanon [AOR = 2.17: 95% CI (1.16-4.08)] were significantly associated with early implanon discontinuation. Women who were counseled about the advantage of implanon [AOR: 0.49: 95% CI (0.28-0.87)] were protective from early implanon discontinuation. Conclusion and recommendation Early implanon discontinuation among mothers was found to be high. Hence, effective counseling on advantages and side effects of implanon and proper management of the side effects should be made to increase implanon retention.