Arboviral and rodent-borne infections are considered a public health concern and pose a significant threat to military service members when deployed in austere environments. In 1990, the U.S. Naval Medical Research Unit (NAMRU) SOUTH, in collaboration with the Peruvian Ministry of Health, initiated febrile illnesses surveillance in Iquitos, Loreto, later expanding to 33 health facilities throughout the country. Additionally, different techniques were developed to maximize virus detection. The activities were crucial in identifying evidence of circulating dengue, Venezuelan equine encephalitis, Mayaro, and Oropouche viruses in the region. Subsequently, Eastern equine encephalitis, encephalomyocarditis, Guaroa, Saint Louis encephalitis, and Rio Mamore viruses, among others, were discovered through our surveillance networks. The results of 3 decades of surveillance identified 16 novel arboviruses and rodent-borne viruses, contributing to public health control and force health protection for the United States and partner nations.