Background Subdermal contraceptive implant is the most widely used method of long-acting reversible contraception among Ethiopian women. Many, however, discontinue use early, which results in unwanted pregnancies and induced abortions and their associated complications. The aim of this study is to determine the rate of and reasons for discontinuation of the contraceptive implant among users in the Kersa district of southwestern Ethiopia. Methods A mixed-method study was carried out between March and April 2019 among 475 women who had been using the contraceptive implant between January 2015 and August 2016 in the Kersa district. Systematic random sampling was used for quantitative data collection and purposive sampling was used for qualitative data collection using 8 focus group discussion and 56 In-depth interviews. A binary logistic regression was carried out for bivariate and multivariable analyses. Results One hundred and ten (23.2 %) contraceptive implant users requested removal before 2.5 years of use. The main reasons for the discontinuation were side effects, followed by a desire for pregnancy or to switch to another contraceptive method and misconceptions. Implant discontinuation was associated with a lack of information prior to insertion on the effectiveness of modern contraception (adjusted odds ratio [OR] 2.0; 95 % confidence interval [CI] 1.13, 3.55), being served by a midwife or nurse (adjusted OR 1.8; 95 % CI 1.04, 3.23), and not being told to return to the health facility if any side effects were experienced (adjusted OR 1.8; 95 % CI 1.01, 3.19) (all p < 0.05). Conclusions Almost a quarter of the study participants discontinued use of the contraceptive implant before the due date. Public health interventions should focus on providing adequate awareness for family planning users, trainings for the health care workers on effective counselling services, especially on side effect and misconceptions.