BACKGROUND: HIV prevention trials usually require that women of childbearing potential use an effective method of contraception. This is because the effect of most investigational products on unborn babies is unknown. We assessed contraceptive use, prevalence and incidence of pregnancy and associated factors among women in a HIV vaccine preparedness study in Masaka, Uganda. METHODS: HIV sero-negative women (18-45 years) at high risk of HIV infection identified through HIV counselling and testing (HCT) were recruited between July 2018 and October 2022. Study procedures included collection of baseline socio-demographics and contraceptive use data, quarterly HCT, counselling on and provision of contraceptive methods onsite/through referral, and 6-monthly urine pregnancy tests. Multivariable Logistic and Poisson regression analyses were conducted to determine factors associated with contraceptive use, prevalence, and incidence of pregnancy. RESULTS: 652 (73%) of 891 women reported contraceptive use at baseline. Contraceptive use was higher in women who were in a relationship/married/cohabiting [adjusted odds ratio (aOR) = 1.60; 95% confidence interval (CI) 1.07-2.40] or divorced/separated/widowed [aOR = 1.86; 95% CI 1.24-2.79] versus those that were single, and among women reporting transactional sex [aOR = 2.10; 95% CI 1.16-3.80] versus those who did not. Baseline pregnancy prevalence was 4% (95% CI 3-6%) and lower in women who reported using long-acting contraceptive methods (aOR = 0.17; 95% CI 0.07-0.39) versus women who did not use these methods. A total of 65 pregnancies over 301.3 person-years of observation (PYO), an incidence rate of 21.6/100 (95% CI 16.9-27.5) PYO, higher among younger women (≤ 24 versus 25 + years, adjusted incidence rate ratio = 1.97; 95% CI 1.15-3.40). CONCLUSION: We observed a high pregnancy incidence in this cohort. Innovative strategies that promote sustained and consistent use of highly effective contraceptive methods especially for young women will be critical to the success of HIV prevention trials in this and similar populations.