Dengue in neonates is an infrequent yet significant cause of neonatal sepsis in endemic areas, often underdiagnosed due to its nonspecific clinical presentation and the lack of specific guidelines for this population. We present a series of three cases of neonatal dengue in patients with fever and signs of late-onset sepsis, who were initially treated with antibiotics without identifying a bacterial agent. Following the diagnosis of dengue through positive IgM, antibiotics were discontinued, and the patients showed favorable clinical outcomes with early hospital discharges. This study highlights the importance of considering dengue as a differential diagnosis in neonates with late-onset sepsis, which could help reduce unnecessary antibiotic use and its adverse consequences. We propose implementing a specific diagnostic algorithm for neonates in endemic regions, including the addition of serological and molecular testing for dengue, to improve management and outcomes in this population.