To evaluate body mass index (BMI) over 36 months among adolescents and young adults using the etonogestrel implant compared with those using depot medroxyprogesterone acetate (DMPA) and a control group. We conducted a retrospective longitudinal cohort study of postmenarchal adolescents and young adults assigned female at birth. The etonogestrel implant and DMPA groups initiated etonogestrel or DMPA between January 1, 2010, and December 31, 2017. Adolescents and young adults in the control group were prescribed a weight-neutral contraceptive or no contraceptive during the same timeframe. The primary outcome of BMI over time was estimated and compared between study groups with inverse probability of treatment weighting linear mixed-effects modeling. Changes in BMI weight category (underweight or normal weight, overweight, obesity) at 12, 24, and 36 months were also explored. Among the 20,409 eligible patients, 860 initiated etonogestrel, 1,817 initiated DMPA, and 17,732 made up the control group. Compared with individuals in the control group, those in the etonogestrel group had a significantly higher mean BMI difference at 9 months (+0.5, P<.01); at 36 months, the mean BMI difference was +1.0 (P<.01). Compared with individuals in the control group, those in the DMPA group had higher mean BMI at 6 months (+0.3, P<.01); at 36 months, the mean BMI difference was +1.3 (P<.01). Regardless of weight changes, increases in BMI weight categories were rare in all groups. Adolescent and young adult patients who initiated the etonogestrel implant demonstrated BMI changes like those on DMPA and higher than control patients; however, these differences may not be clinically concerning. This study provides important information that can help in counseling adolescent and young adult patients about expectations when starting and using etonogestrel.