Introduction Efficient resource allocation in surgery requires thorough economic evaluation that reflects the true costs of a procedure, with micro-costing being a primary method. Existing economic studies on microvascular jaw reconstruction of the jaw often exclude or estimate key cost-drivers. The aim of this study was to estimate the direct financial costs and cost-drivers associated with surgical reconstruction of the jaw from the perspective of the healthcare provider. Methods A retrospective micro-costing study from the perspective of the healthcare provider was performed on 100 patients who underwent mandibular or maxillary free flap reconstruction. Direct financial costs of activities (in USD) from admission to discharge were examined, and classified into operative and perioperative admission periods. Results The mean cost for the entire admission was $36,415.95 ± 14,246.56 comprising 57.7% from the operative period and 42.3% from the perioperative admission period. Ward staffing and consumables (35.7%), prostheses (25.0%), and operating room staffing (21.0%) were the largest cost contributors. In adjusted analyses, higher costs were associated with vasculopathy (+$9,142.02, p=0.044), ASA IV ($19,495.93, p=0.023), tracheostomy (+$10,445.81, p=0.012), return to the operating room (+$19,920.22, p=0.005), and return to the intensive care unit (+$25,316.26, p=0.014). Conclusion Jaw reconstruction is associated with considerable direct financial costs to the healthcare provider with complications requiring return to the operating room and/or return to the intensive care unit the critical key cost-drivers. These insights will support future health technology assessments focused on jaw reconstruction to assist decision-makers in implementing or reimbursing these procedures.