In Kenya many people who have been affected by sexual violence turn to the health sector for clinical treatment and preventive therapies. This interface provides a vital opportunity to impact on the dual epidemics of HIV and sexual violence. Despite this, the uptake of post-rape care services in health facilities is low and health care providers felt ill-prepared to deal with the consequences of sexual violence. A qualitative study was conducted to better understand the reasons for the low uptake of services and to establish perceptions of sexual violence in Kenya. Thirty-four key informants were interviewed and sixteen focus group discussions with women and men were held in three districts in Kenya. Blurred boundaries between forced and consensual sex emerged. Important implications for the delivery of HIV post exposure prophylaxis (PEP) after sexual violence include the need for gender-aware patient-centred training for health providers and for HIV PEP interventions to strengthen on-going HIV-prevention counselling efforts. Further research needs to determine the feasibility of on-going risk reduction measures in the context of PEP delivery.