BackgroundThe United Nations has set a target of ending the HIV/AIDS epidemic as a public health threat by 2030. The WHO recommended the use of oral pre-exposure prophylaxis (PrEP) for HIV prevention for all people at substantial risk of HIV infection in 2016. In Namibia since the adoption of PrEP in 2016, many clients have been initiated on PrEP. ObjectivesThe objectives of this study were to measure clients’ rate of PrEP retention at three months and determine factors that influence it in the Omusati region of Namibia. MethodsAn analytical cross-sectional design was used for this study. Three hundred and forty-five participants were selected for this study using a simple random sampling method. The data were collected from the Electronic Patient Monitoring System (EPMS). Chi-square tests and logistic regression were used for data analysis. ResultsThe retention rate in PrEP care at three months was 60 %. The Chi-square tests showed significant associations between age, sex, sexually transmitted infection (STI) symptoms, marital status, HIV status and viral load of partner, number of sexual partners, and retention in PrEP care at three months (p < 0.05). Logistic regression analysis revealed that females and those with STI symptoms were more likely to be retained in PrEP care, Adjusted Odds Ratio (AOR) = 2.21, 95 % CI (1.36–3.57), and AOR = 4.25, 95 % CI (1.23–14.63), respectively. Participants with HIV-negative/unknown status partners and with multiple/concurrent sexual partners were less likely to continue with PrEP, Crude Odds Ratio (COR) = 0.56, 95 % CI (0.36–0.86), COR = 0.39, 95 % CI (0.16–0.96), respectively. ConclusionThe findings of this study accentuate the need for increased provision of information on the importance of the continuation of PrEP.