We aimed to elucidate the role of intraoperative clean surgical margin (iCSM) determined according to lesion size and duration to obtain appropriate histological clean surgical margin (hCSM) in high-risk basal cell carcinoma (BCC) patients evaluated according to National Comprehensive Cancer Network (NCCN) criteria considering the tumor size and/or location. The contribution of lesion area to determine iCSM was also evaluated. Patients with high-risk BCC requiring surgical management were included. iCSM, hCSM, and clinical variables including sec, age, longest edge, location and area, and follow-up duration were recorded. In total, 96 lesions were evaluated. Lesions were mostly located in the mask area and other face region (93.8%). Lesions located on the nose comprised 50%, 34.1%, and 26.3% in the BCC-5, BCC-7, and BCC-10 lesions, respectively. The hCSMs were positive in 11.5%, 9.1%, and 3.8% of the BCC-5, BCC-7, and BCC-10 lesions, respectively. The deep surgical margin was positive in 15.4%, 4.5%, and 7.7% of the BCC-5, BCC-7, and BCC-10 lesions, respectively. The calculated risk for the positive surgical margin if the BCC-10 lesions were done like the BCC-7 was 15.4%. No recurrence was during follow-up duration. As supported by the findings of the present study, to obtain an adequate hCSM in the high-risk BCC lesions, the iCSM determined according to NCCN recommendations may not be optimal. Nevertheless, after their categorization according to lesion size and disease duration for excision with 5-, 7-, and 10-mm iCSMs, it is possible to obtain a small but important improvement in the outcome of patients.