Background The etonogestrel implant Implanon is a favourable and cost-effective contraceptive method for women in developing countries, and expansion of its use represents a priority for the family planning (FP) programme in Egypt. We studied the factors affecting first-year Implanon discontinuation from clients' and providers' perspectives. Methods We used a mixed quantitative-qualitative methodology. We conducted a household survey of Implanon clients and three focus group discussions with FP physicians and directors. Results We found that 13.5% of Implanon users discontinued its use in the first year. Survival analysis found that clients who had previously used Implanon (HR 0.36, 95% CI 0.15 to 0.88) and whose husbands had secondary or a higher level of education (HR 0.36,95% CI 0.19 to 0.69) were less likely to discontinue Implanon use after the first year, while clients who experienced side effects of Implanon use were more likely to discontinue it (HR 3.6,95% CI 1.60 to 8.11). Other causes of discontinuation which emerged in the qualitative analysis were the unjustified advice for Implanon removal by non-gynaecologists, due to unrelated users' complaints, and deficient pre-insertion counselling. Conclusions Implanon has a low first-year discontinuation rate as compared with other contraceptive methods. FP clients should be given sufficient pre-insertion counselling about side effects of Implanon and duration of protection. Physicians should offer Implanon mainly to clients seeking long-term contraception in order to decrease its discontinuation rate and increase its cost effectiveness.