Pregnancy is the second most common cause of limited duty days among active duty service members in the U.S. Military. Pregnancy accounts for 10% of all days on restricted duty, despite impacting a minority of active duty service members. One out of five service women will experience an unintended pregnancy every year despite the availability of no-cost contraception and reproductive healthcare. Young, single, junior enlisted service women experience the highest rate of unintentional pregnancy. Previous studies have demonstrated service branch-based variability in selection, initiation, and continuation of specific contraceptive methods related to service branch culture and access to contraception during basic training. It is unclear if these differences impact overall contraception use or fertility rates among junior enlisted service women in their first term of enlistment. This study examines rates of contraceptive selection, initiation, continuation, and efficacy among junior enlisted service women in their first 4-year enlistment period, and the service branch specific variability in these outcomes. This study is a secondary analysis of Military Healthcare Data Repository records from women who began basic training between 2012 and 2020 and remained on active duty for at least 12 months. We used Kaplan-Meier analyses to examine the effect of age and military branch on contraceptive continuation and efficacy. We used binomial regression for interval censored data, to assess the association of service branch with rates of contraceptive initiation, contraception use, births, and childbirth-related duty restrictions. We identified 147,594 women who began basic training between 2012 and 2020. The mean age of these women at the beginning of basic training was 20.4 ± 3.1 years. Women in the marines and navy had higher contraceptive initiation rates than women in the army or air force. Among women initiating a contraceptive pill, patch, or ring (short-acting reversible contraception), 58.3% were still using some form of hormonal contraception 3 months later. Among women initiating depot-medroxyprogesterone (DMPA), 38.8% were still using any form of hormonal contraception 14 weeks later. Long-acting reversible contraceptive methods, such as intrauterine or subdermal contraceptives, had higher continuation rates and less service-based variability in continuation and failure rates than short-acting reversible contraception or depot-medroxyprogesterone. The proportion of days on any form of prescription contraception during the first 4 years on active duty varied from 23.3% in the army to 38.6% in the navy. The birth rate varied from 34.8 births/1,000 woman-years in the air force up to 62.7 births/1,000 woman-years in the army. Compared with women in the air force, women in the army experienced 2,191 additional days of postpartum leave and 13,908 days on deployment restrictions per 1,000 woman-years. Service branch specific variability in contraceptive use is associated with differences in days of pregnancy-related duty restrictions during first 4 years on active duty among junior enlisted females. Robust implementation of best practices in contraceptive care across the military health system to improve contraceptive initiation and continuation appears to offer an opportunity to improve military readiness and promote the health and well-being of active duty service women, particularly in the army.