Objective/Hypothesis: To appraise the utility of a novel EMR-based checklist for complex head and neck microvascular free-tissue reconstruction. Study Design: A prospectively collected retrospective matched cohort study from a single tertiary care academic institution. Methods: A retrospective matched cohort study from an academic tertiary care center with 76 total patients analyzed for disease-specific and quality outcomes before and after implementation of an EMR-based checklist tailored to complex head and neck care. The intervention group consisted of 38 consecutive patients undergoing microvascular free tissue reconstruction after implementation of the EMR-based checklist strategy. A historic cohort of 38 patients was derived by matching patients meticulously for disease-specific and surgical characteristics. Primary outcomes included post-operative medical and surgical complications, intensive care requirements, 30-day reoperation rates, hospital length of stay, and completion of preoperative metastatic evaluations. Secondary outcomes included patterns of antibiotic administration, ultimate discharge dispositions, flap survival, and recognition of preoperative hypothyroidism in previously radiated patients. Results: Implementation of the perioperative checklist yielded an overall reduction in major medical complications (10.5% vs. 29.0%, P <.05*), post-operative antibiotic administration (17.4% vs. 44.7%, P <.05*), hospital length of stay (median (IQR) days 6 (1) versus 7 (3.25), P <.05*), and improved metastatic evaluation completion (92.1% vs. 63.2%, P <.05*). There was an improved discharge disposition (92.1% vs. 73.7%, P <.05*). No difference was observed in major wound complications (50.0% vs. 57.9%, P =.49), 30-day re-operation rates (31.5% vs. 34.2%, P =.81), 30-day readmission rates (21.1% vs. 21.1%, P >.99), escalations to intensive-care (13.2% vs. 21.1%, P =.36), or flap survival (97.4% vs. 89.5%, P =.17). Conclusions: Use of our EMR-based perioperative checklist reduced major medical complications, post-operative antibiotic administration, hospital length of stay, and improved discharge outcomes for patients undergoing microvascular free-tissue reconstruction. Level of Evidence: 3 Laryngoscope, 131:E2251–E2256, 2021.