Background: Mosquito-borne infections are of global health concern because of their rapid spread and upsurge, which creates a risk for coinfections. Chikungunya, an arbovirus disease transmitted by Aedes aegypti or A. albopictus, and malaria, a parasitic disease transmitted by Anopheles gambiae, are prevalent in Nigeria and neighbouring countries, but their burden and possible coinfections are poorly understood. In this study, we investigated the seroprevalence, hidden burden and endemicity of chikungunya and malaria in three regions in Nigeria. Methods: A cross-sectional sero-survey was conducted on 871 participants in three regions of Nigeria. The samples were collected from outpatients employing simple random sampling. All serum sample analyses were performed using CHIKV virus-like particle recomLine Tropical Fever for the presence of arboviral antibody serological marker IgG immunoblot for chikungunya and malaria RDT (Rapid Diagnostic Test) for malaria parasites. Results: The seroprevalences of chikungunya and malaria mono-infection were 64.9% and 27.7%, respectively, while the coinfection seroprevalence was 71.9%. The central (69.5%) and northern (67.0%) regions showed more significant seroprevalences than the southern region (48.0%). The seroprevalence and the hidden burden of chikungunya and malaria infections varied across the three geographical regions. Conclusions: This study highlighted an unexpectedly high seroprevalence and hidden endemicity of chikungunya and a less surprising high malaria endemicity in three regions of Nigeria.