Rift Valley fever virus (RVFV) is an arthropod-borne phlebovirus reported to be circulating in most parts of Africa. Since 2009, RVFV has been suspected of continuously circulating in the Union of Comoros. To estimate the incidence of RVFV antibody acquisition in the Comorian ruminant population, 191 young goats and cattle were selected in six distinct zones and sampled periodically from April 2010 to August 2011. We found an estimated incidence of RVFV antibody acquisition of 17.5% (95% confidence interval (CI): [8.9–26.1]) with a significant difference between islands (8.2% in Grande Comore, 72.3% in Moheli and 5.8% in Anjouan). Simultaneously, a longitudinal entomological survey was conducted and ruminant trade-related information was collected. No RVFV RNA was detected out of the 1,568 blood-sucking caught insects, including three potential vectors of RVFV mosquito species. Our trade survey suggests that there is a continuous flow of live animals from eastern Africa to the Union of Comoros and movements of ruminants between the three Comoro islands. Finally, a cross-sectional study was performed in August 2011 at the end of the follow-up. We found an estimated RVFV antibody prevalence of 19.3% (95% CI: [15.6%–23.0%]). Our findings suggest a complex RVFV epidemiological cycle in the Union of Comoros with probable inter-islands differences in RVFV circulation patterns. Moheli, and potentially Anjouan, appear to be acting as endemic reservoir of infection whereas RVFV persistence in Grande Comore could be correlated with trade in live animals with the eastern coast of Africa. More data are needed to estimate the real impact of the disease on human health and on the national economy., Rift Valley fever (RVF) is a viral disease transmitted by mosquitoes to ruminants. The disease may affect humans and has a great impact on the economy of the affected country. RVF occurs mostly in African countries, but epidemics have been reported in Madagascar and in the Arabian Peninsula. In the Union of Comoros, RVF virus (RVFV) has been suspected of continuously circulating since 2009 without any notifications of the typical clinical signs by the Comorian Animal Health Services. From April 2010 to August 2011, we conducted a livestock longitudinal survey in Grande Comore, Moheli and Anjouan. Our study aimed to detect RVFV-specific antibody acquisitions in cattle and goats. Simultaneously, a longitudinal entomological survey was conducted to describe the diversity of mosquitoes in the study zones and ruminant trade-related information was collected. Our investigations showed that Comoros ruminants acquired RVFV-specific antibodies all along the year and particularly in Moheli during the dry season. Our findings suggest a complex RVFV epidemiological cycle in the Union of Comoros with probable inter-islands differences in RVFV circulation patterns. The disease appears to be endemic in Moheli and potentially Anjouan, but the persistence of the disease in Grande Comore could be correlated with trade in live animals with the eastern coast of Africa.