As other febrile diseases, dengue was considered as differential diagnosis due the presence of the vector and previous DENV reports in Burkina Faso. To explore the virus presence in acute febrile non-malaria cases and Aedes mosquitoes in Ouagadougou, an exploratory cross sectional study was performed from December 2013 to January 2014. Five sectors and six correspondent health care centers (CSPS) were selected based on reported presence of Flavivirus. A survey about symptoms was administered to the participants and finger pricks were used to obtain the samples. Each CSPS tested every febrile non-malaria patient for dengue using dengue rapid tests (SD Bioline DengueDuo). Blood spots were collected in filter paper from all positive results and every tenth negative for further PCR analyses. A parallel entomological survey was conducted in the CSPS’s corresponding sectors. From a total of 379 tested patients, 33 (8.7%) were positive for rapid test (60% both IgM/IgG; 21% just IgG and 5% just NS1). From 60 samples tested by RT-PCR, 15 were positive (9 from positive rapid test and 6 from the subsample of negative results). The serotypes observed were DENV2, DENV3 and DENV4. There was no DENV in the analyzed mosquitoes’ sample.These findings have important public health implications in order to prepare the health system and the population for dengue’s presence and outbreaks prevention.