The global incidence of dengue has grown dramatically in recent decades. In Burkina Faso, the last description of acute cases was back in 1982. During an annual population-based survey in Kaya and Zorgho, two semi-urban areas, febrile individuals from 0-10 years old were evaluated for malaria and dengue virus (DENV). Rapid tests were performed and additional samples on filter paper were taken from every patient with a positive result and every tenth negative, to perform reverse transcription-polymerase chain reaction (RT-PCR) assays. From 259 children (150 in Kaya and 109 in Zorgho), 52.1% were positive for malaria and 6.9% for dengue while 45.2% remained undifferentiated. The RT-PCR results show the presence of DENV2 and DENV4. These findings reveal the presence of DENV in the country and the need to conduct research and actions on non-malaria febrile diseases in the region.