Pneumonia, sepsis, and meningitis are three of the main causes of hospitalization and mortality, particularly in children under 5 years old. The economic burden associated with these illnesses is important for health policy, planning, and management. We investigated the cost of pneumonia, sepsis, and meningitis in hospitalized children younger than 5 years of age at a tertiary public hospital. The study was designed as an incidence-based cost of illness study from a societal perspective. Data were collected from medical records and prospective interviews from October to November 2014. Forty patients were included, comprising patients with pneumonia (35 cases), sepsis (3 cases), and meningitis (2 cases). The mean total costs (SD) of illness per episode were US $1,945 (2,628), US $3,489 (2,757), and US $4,855 (28,360) for pneumonia, sepsis, and meningitis, respectively. High economic burden of pneumonia, sepsis, and meningitis in children was found. These data could help policymakers evaluate the cost-effectiveness of vaccination strategies against these illnesses.