Background: Rift Valley fever (RVF) is a mosquito-borne viral zoonosis currently confined to the African continent and the Arabian Peninsula. This study aimed to estimate the prevalence of antibodies to RVF virus (RVFV) in cattle and goats in an area affected by the 2010-2011 outbreaks and to identify factors associated with seropositivity. Methods: A cross sectional study was conducted during 2015/2016 in a 200 km × 200 km area between Bloemfontein and Kimberley in the Free State and Northern Cape Provinces. Sampling points were selected using random geographic points with probability proportional to density of livestock-owning households. Up to nine cattle and goats were randomly sampled from the farm closest to each selected point. A questionnaire was used to collect information concerning animal, management, and environmental factors. Serum samples were screened for RVFV antibody using IgG indirect ELISA and inhibition ELISA was used for confirmation. Data were analyzed separately for each species by univariable screening followed by multilevel logistic regression models. Results: A total of 956 cattle and 520 goats were sampled from 232 farms. Overall RVF seroprevalence, adjusted for clustering and sampling weight, was 25.5% (95% CI: 20.8, 30.9%) in cattle and 7.5% (95% CI: 4.3, 12.7%) in goats. Seroprevalence in cattle was highest in Brandfort (50.0%) and Bultfontein (43.5%), and in goats in Jagersfontein (22.2%) and Koffiefontein (11.4%). Seroprevalence in cattle was higher in animals older than 4 years, in dairy cattle, in animals not kraaled at night, on farms that had seasonal pans, and on farms recently (2014-2016) vaccinated against RVF. In goats, seroprevalence was higher in animals older than 4 years, on private compared to communal farms, and on farms with seasonal pans or permanent rivers or dams, and lower on farms with man-made dams. Conclusion: Seroprevalence was higher in cattle than in goats, but in both species the level of herd immunity four years after the last reported outbreaks was low. Associations with known environmental risk factors for RVF transmission indicate the possibility that viral circulation has taken place during the inter-epidemic period.