Background <p>Persistent high-risk human papillomavirus (hrHPV) infection after hysterectomy or residual cervix resection for incompletely excised cervical intraepithelial neoplasia grade 3 (CIN3) remains a clinical concern. However, the factors associated with postoperative hrHPV positivity in this setting are not well characterized.</p> Methods <p>This retrospective study included 288 patients who were treated between 2014 and 2024. We evaluated factors associated with postoperative hrHPV positivity after hysterectomy or residual cervix resection for incompletely excised CIN3. Patients were grouped according to their hrHPV status at the first postoperative follow-up, and associated factors were identified by using logistic regression.</p> Results <p>At the first postoperative follow-up, 50 patients (17.4%) were hrHPV positive. According to the univariate analysis, postoperative hrHPV positivity was associated with ectocervical margin involvement, older age, and lower gravidity (all <i>p</i> &lt; 0.05). Multivariate analysis revealed that ectocervical margin involvement remained independently associated with postoperative hrHPV positivity (OR 5.273, 95% CI 1.491–18.640; <i>p</i> = 0.010). For the patients who were hrHPV positive at the first postoperative follow-up, subsequent clearance of infection mostly occurred within 2&#xa0;years after surgery.</p> Conclusions <p>Ectocervical margin involvement was associated with a higher likelihood hrHPV positivity at the first follow-up after hysterectomy or residual cervix resection for incompletely excised CIN3. This observation warrants confirmation in future prospective studies.</p>