Abstract Background Etonogestrel and levonorgestrel contraceptive implants, though safe, but exhibits adverse effects severe enough to necessitate discontinuation. Objective This study intends to compare the complication rates, and reasons for discontinuation of etonogestrel and levonorgestrel contraceptive implants, at Niger Delta University Teaching Hospital (NDUTH) Method and materials It was a retrospective cross-sectional study of 1232 women who used etonogestrel and levonorgestrel contraceptive implants, and discontinued during the study period. A total of 324 women used etonogestrel implants, while 908 used levonorgestrel. Data collected was: Socio-demographic characteristics, the duration of contraceptive use, the complications experienced, and the reasons for implant removal. Results The mean age of the women who took etonogestrel implants was significantly higher than that for levonorgestrel, t = 3.99(0.85, 2.49), p = 0.0001. Regarding parity, significantly more women of very high parity (grand multiparous women) took etonogestrel p = 0.007. While more of nulliparous women took levonorgestrel implants p = 0.005. The mean duration of contraceptive use was significantly higher among women who used levonorgestrel implant, t = 2.23, p = 0.02, and more women replaced etonogestrel implant than levonorgestrel, odds ratio = 17.43[10.83, 28.05], p = 0.001. Compared to levonorgestrel implants, women who used etonogestrel significantly had more complications, p = 0.002, especially vaginal bleeding (p = 0.002), weight gain (p = 0.0001), and breast pain (p = 0.001). Expired implant (44.7%) was the commonest reason for removal, and the rate was significantly higher among women who used levonorgestrel, p = 0.001.There was no difference in the discontinuation (from complications) between the two groups, except heavy vaginal bleeding, which was twice higher among those who used etonogestrel, odds ratio = 2.59[1.85, 3.63], p = 0.001. Conclusion Etonogestrel implant has more complications than levonorgestrel, especially irregular vaginal bleeding, weight gain, and breast pain. Keywords: etonogestrel, levonorgestrel, implants, complications.