The burden of Arboviral infections is largely underestimated in Africa, particularly in North-Eastern Nigeria. A total of 200 serum samples were collected from patients exhibiting febrile illness who visited the State Specialist Hospital in Maiduguri for medical attention between March and April 2018. Sera were tested for Flavivirus RNA by a pan-flaviviral primer set using hemi-nested RT PCR. Twenty-six samples were positive for flaviviral RNA and sequence analysis indicated a high number of West Nile virus infections and one case of Zika virus. In-house recombinant NS1-based IgM ELISA indicated 47% of WNV and 22% of ZIKV infections. These data were also compared to commercially available assays for West Nile and Zika virus. Finally, NS1 IgG ELISA was conducted for Dengue, Zika, West Nile and Usutu viruses. For serum samples detected by at least one flavivirus, 94,5% tested positive by NS1 IgG antibodies, while only 5.5% of the patients were negative for all. To conclude, there is a high prevalence rate of arbovirus infections in the region, including Zika and Usutu viruses that were not previously detected. Interestingly, the analysis was conducted using in-house tools to allow the implementation of a sustainable surveillance protocol locally.Copyright © 2020. Published by Elsevier B.V.