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Objectives: This study analyzed the costs associated with healthcare professionals’ care for patients with Severe Acute Respiratory Infections (SARI) due to COVID-19 at the Brasília University Hospital (HUB) during the Public Health Emergency (PHE). Methods: The Time-Driven Activity-Based Costing (TDABC) methodology was used to estimate costs based on the time and remuneration of shift-based and non-shift-based professionals, across wards and PHE phases. Sociodemographic and clinical data were extracted from electronic medical records, and a multivariate analysis was conducted to identify cost predictors. Results: The total cost of the 627 hospitalizations was R$10,391,881.31, with Phase 5 (July–December 2021) having the highest expenditures, accounting for over 50% of the total costs. The yellow ward (general ward) had the highest total costs (40.3%), followed by the red ward (intensive care unit with mechanical ventilation) and the orange ward (intensive care unit without mechanical ventilation). The median per-patient cost varied significantly between the wards. The red ward had the highest median cost (R$7,269.38; IQR R$2,849.77–15,310.70). Multivariate analysis identified age (0.6% cost increase per year), female (19% increase compared to males), patient origin (55.2% higher when referred from another hospital; 72.4% higher when transferred from another HUB sector), and length of stay (4.7–5.5% cost increase per additional day, depending on ward) as significant predictors of increased costs. Conclusions: This study reveals the complex and substantial costs associated with healthcare professionals' provision of hospital care for patients with COVID-19-related SARI during the PHE.