Neonatal infections contribute to high mortality, yet data describing neonatal sepsis are predominantly from high-income countries. Epidemiology is likely to vary across settings, potentially affecting the way infections are managed. We aimed to describe the epidemiology of clinically-suspected infection in neonates ( < 28 days of age) at the Philippine General Hospital in Manila, Philippines. We undertook prospective surveillance enrolling all neonates admitted to the Neonatal Intensive Care Unit (NICU) who had at least one episode of clinically-suspected infection between November 2023 and November 2024. We enrolled 799 neonates with 1,024 episodes of clinically-suspected infection. We found that only 1% of suspected early onset infections ( < 48 hours of life) returned a positive blood culture (6/757). 15% of neonates died (117/799), including 12% (93/754) of those with suspected a suspected infection that didn't return a positive culture and 53% (24/45) of those with confirmed culture-positive infections. We found a significant burden of culture-negative clinically-suspected infection and high mortality. There is a great need to improve case definitions and diagnostic capacity for neonatal infection and to reduce antibiotic overuse, in order to provide effective treatment and improve clinical outcomes for neonates.