Background: Basal cell carcinoma (BCC) is the most common type of eyelid malignancy and it is considered to be dangerous due to its proximity to functionally essential organs. Early diagnosis and complete excision of the primary lesion are crucial to prevent infiltration and metastasis. The study aims to evaluate the extent of recurrence in subjects affected by BCC of the upper third of the face treated with surgical eradication and the frozen section technique with complete margin control (CMC-FS), in comparison with the gold standard Mohs micrographic surgery (MMS). Materials and Methods: The study included 111 patients with 111 biopsy-proven eyelid BCCs. On clinical examination, all lesions were removed with 2 mm margins clinically free of neoplasm. Prior to reconstruction, CMC-FS analysis of all surgical margins was performed on each tumor for histopathologic confirmation. Subsequently, all margins were presented for the permanent paraffin sections. Results: There were 69 primary carcinomas and 42 secondary carcinomas among the 111 samples. No recurrence occurred in 109 tumors followed-up for at least 5 years, with a total recurrence rate of 1.8%. The median time between lesion excision and diagnosis of recurrence was 20 months. Conclusions: at 5-year follow-up, CMC-FS guided excision of BCCs of the eyelids resulted in recurrence rates equivalent to MMS. Intraoperative microscopic control of all margins reduced the recurrence rate of the upper third of the facial BCCs, correlating with easier reconstruction with better esthetic and functional outcome.