In 2017, Kenya became one of the first African countries to provide pre-exposure prophylaxis (PrEP) in its national HIV prevention plan. We sought to characterize factors associated with PrEP uptake and persistence among a cohort of women at risk of HIV infection during the early stages of PrEP scale-up in Kenya. HIV-negative women ≥18 years with ≥2 sexual partners in the past 4 weeks were recruited as part of an ongoing cluster randomized trial of an HIV self-testing intervention. PrEP use was assessed at baseline and at 6- and 12-month follow-up visits. Between June 2017 and August 2018, 2,086 were enrolled and had complete baseline data. 138 (6.6%) reported PrEP use during the first year of the study. Although PrEP use increased, persistence on PrEP was low, and less than half of individuals reported continuing PrEP at follow-up visits. In multivariate analyses, PrEP use was associated with recent STIs, having an HIV-positive primary partner, having regular transactional sex in the past 12 months, and being a female sex worker. In the early stages of PrEP scale-up in Kenya, uptake increased modestly among women with risk factors for HIV infection, but overall uptake and persistence was low.