To estimate the economic burden of Severe Acute Respiratory Infection (SARI) in lab-confirmed influenza patients from a low-income country setting such as Colombia. A bottom-up costing analysis, from both third payer and social perspectives, was conducted. Direct costs of care were based on the review of 227 clinical records of lab-confirmed influenza inpatients in six facilities from three main Colombian cities. Resources were categorized as: length of stay (LOS), diagnostic and laboratory tests, medications, consultation, procedures, and supplies. A survey was designed to estimate out-of-pocket expenses (OOPE) and indirect costs covered by patients and their families. Cost per patient was estimated with the frequency of use and prices of activities, calculating median and 95% confidence intervals (95% CI) with bootstrapping. Total costs are expressed as the sum of direct medical costs, OOPE and indirect costs in 2018 US dollars. The media direct medical cost per SARI lab-confirmed influenza patient was US$ 700 (95% CI US$ 552-809). Diagnostic and laboratory tests correspond to the highest cost per patient (37%). Median OOPE and indirect costs per patient was US$ 147 (95% CI US$ 94-202), with the highest costs for caregiver expenses (27%). Total costs were US$ 848 (95% CI US$ 646-1,011), OOPE and indirect costs corresponded to 17.4% of the total. The median of direct medical costs per patient was three times higher in elderly patients. SARI influenza costs impose a high economic burden on patients and their families. The results highlight the importance of strengthening preventive strategies nationwide in the age groups with higher occurrence and incurred health costs.