Background/Objectives: To ensure that non-melanoma skin cancer (NMSC) is completely removed in healthy tissue, micrographically controlled surgery (3D histology) is often performed, which can prolong the inpatient stay. This study examined ex vivo reflectance confocal microscopy (evRCM) for perioperative assessment of surgical margins, specifically in cases where re-excision was necessary due to incomplete removal of cutaneous tumor tissue. Methods: NMSC re-excisions were evaluated using evRCM by a cutaneous surgeon, with retrospective review by an independent pathologist when results differed from histology. Results: evRCM demonstrated high specificity (0.96; 95% CI, 0.90–0.99) but low sensitivity (0.20; 95% CI, 0.06–0.51). Unlike pathology, which discards outer surgical margins, evRCM examined the true surgical margins. Retrospective pathology analysis of the misdiagnosed cases confirmed that 25% (n = 2/8) were false negative and 75% (n = 6/8) were potentially false positive, resulting in a sensitivity of 0.2–0.8. Notably, evRCM led to a 113-day reduction in in-hospital stays, probably resulting in increased patient satisfaction and cost-effectiveness. Conclusions: evRCM was valuable for speeding up the assessment of surgical margins in patients with re-excised NMSC. Proper tissue preparation and assessment require interdisciplinary collaboration between cutaneous surgeons, pathologists, and physician assistants, emphasizing the need for standardized operating procedures.