The study examined the prevalence of dengue virus (DENV) and Chikungunya virus (CHIKV) in the Horn of Africa through a systematic review and meta-analysis of 65 studies, with the majority from Kenya (63.1%), followed by Ethiopia (30.8%) and Somalia (6.1%). Overall dengue prevalence was 20% for IgG antibodies, 10% for IgM, 6% for NS1 antigen, and 4% by PCR testing. Chikungunya prevalence was 5% for IgG, 8% for IgM, and 4% by PCR. All four dengue serotypes circulated in Kenya and Ethiopia, while only DENV-2 and DENV-3 were reported in Somalia. The Aedes aegypti mosquito was the predominant vector, identified in 92.3% of vector studies. The disease burden is likely underrecognized and represents a growing public health threat in the region.