Dengue and chikungunya are widely distributed in Cameroon but there is still not enough information on their prevalence in different epidemiological settings. This study was undertaken to assess dengue and chikungunya prevalence in both urban and rural settings in Cameroon using 3 diagnostic tools. From December 2019 to September 2021, willing febrile (temperature >38°C) outpatients visiting 4 healthcare facilities in the cities of Yaoundé and Dizangué were screened for dengue and chikungunya. Clinical symptoms were recorded and blood samples collected in EDTA tubes were centrifuged to obtain plasma, then analysed using rtRT-PCR, RDTs and ELISA. Odds ratios were used to determine the level of association between socio-demographic factors, clinical features and the infection status. Kappa statistic permitted to assess the level of agreement between RDTs and ELISA. Overall, 301 patients were recruited: 198 in Yaoundé and 103 in Dizangué. The prevalence varied according diagnostic tool. For dengue, 110 patients were positive to rtRT-PCR: 90 (45.45%) in Yaoundé and 20 (19.42%) in Dizangué. The prevalence of dengue IgM using ELISA varied from 22.3% in Dizangué to 30.8% in Yaoundé. Dengue positivity rate using RDTs was 7.6% in Yaoundé and 3.9% in Dizangué. For chikungunya, one (0.5 %) patient (Yaoundé) was tested positive to rtRT-PCR. The prevalence of chikungunya IgM with ELISA varied from 18.4% in Dizangué to 21.7% in Yaoundé, while using RDTs, it was 4.5% in Yaoundé and 12.6% in Dizangué. RDTs for either chikungunya or dengue displayed very poor sensitivity. Abdominal and retro-orbital pains were significantly associated to acute dengue infection. All the four dengue serotypes were recorded with a predominance of DENV-3 (35.45%) and DENV-4 (25.45%). This study further confirms endemicity of both dengue and chikungunya in Yaoundé and Dizangué. These data stress the need for active surveillance of cases to prevent outbreaks occurrence across the country.