This study aimed to determine whether endocervical glandular involvement (GI) affects the clinical prognosis of patients with cervical intraepithelial neoplasia (CIN) III who underwent the loop electrosurgical excision procedure (LEEP). This retrospective study included 250 patients who underwent LEEP for the treatment of CIN III between August 2005 and May 2020. The medical records of 234 patients were analyzed; 137 (58.5%) patients were GI negative, and 97 (41.5%) were GI positive. Margin involvement of the LEEP specimen was found in 59 (45.4%) patients in the GI-negative group and 54 (58.7%) patients in the GI-positive group (p = 0.051). The additional surgical procedures (repeat conization or hysterectomy) were significantly more performed in GI-positive patients than in GI-negative patients (40.9% vs. 23.1%, p = 0.004). When comparing the LEEP specimens of GI-1 (GI-positive confirmed via cervical biopsy before conization) and GI-2 (GI-positive confirmed via conization), we found that the mean depth was significantly greater in the GI-1 group (10.9 mm) than in the GI-2 group (7.6 mm) (p = 0.024). Surgical margin involvement was more frequently observed in the GI-2 group than in the GI-1 group (p = 0.030). There was no significant difference in the recurrence rates of CIN between the GI-negative and GI-positive groups (p = 0.641). In conclusion, despite no significant differences in residual disease and CIN recurrence between the GI-negative and GI-positive groups, additional surgical treatments were more frequently performed in GI-positive patients. Repeat surgery based on GI positivity should be carefully considered to avoid overtreatment and surgical complications.