Dengue and Zika are arboviruses transmitted by the Aedes aegypti mosquito and cause high morbidity and mortality rates. This study aimed to identify epidemiological and clinical factors related to dengue and Zika in febrile patients in the Lambayeque region of Peru from July 2022 to June 2023. This was a prospective observational cross-sectional study of 403 patients. Arboviruses were diagnosed serologically by enzyme immunoassay using NS1 antigen markers and IgM antibodies against dengue and Zika viruses. Clinical and epidemiological data were collected using clinical-epidemiologic research forms. The sample was characterized by a mean age of 31 years and 46.4% male. Headache (71.7%), myalgia (57.1%), and hand arthralgia (54.1%) were the most common symptoms. The prevalence of dengue and Zika was estimated at 19.9% and 3.4%, respectively. Patients from the province of Ferreסafe (RPa = 2.15, P = 0.011), those who reported no history of the disease (RPa = 2.99, P = 0.002) and those who reported low back pain (RPa = 1.75, P = 0.015) were more likely to present dengue. Comorbidities were associated with Zika (ORa = 13.57, P = 0.012). Dengue and Zika are prevalent arboviruses in febrile patients in the Lambayeque region of Peru, where the origin, lack of history, comorbidities, and some clinical manifestations are associated with a greater likelihood of these diseases.