To analyze the outcome and risk factors of recurrence in patients with basal cell carcinomas (BCCs) of the eyelid treated by en face frozen section-controlled (FSC) excision with a mean follow-up over 5 years. This was a retrospective series of 108 patients with 110 biopsy-proven eyelid BCCs. All lesions were excised with 2 mm margins clinically free from neoplasia at clinical examination. For each tumor, en face frozen section examination of surgical margins was employed for the histologic confirmation before the reconstruction. Subsequently, all margins were submitted for permanent paraffin sections. Of 110 malignancies, 80.9% represented primary carcinomas and 19.1% secondary ones. The overall recurrence rate was 1.8%, with a mean follow-up of 72.4 months (range 30-167). The mean time between the excision of the lesion and the diagnosis of the recurrence was 24 months (range 20-28). No recurrences were observed in 62 tumors followed up for at least 5 years. Secondary BCCs were associated with a higher recurrence rate compared with primary BCCs (4.8% and 1.1%, respectively, p = 0.262). The FSC excision of eyelid BCCs yields recurrence rates comparable to those of Mohs micrographic surgery at 5-year follow-up. Intraoperative microscopic margin control improves the cure rate of eyelid BCCs, and FSC excision with small margins (2 mm) clinically free from neoplasia is associated with easier reconstruction and better cosmetic and functional outcomes.