Background and Objectives: In women who are positive for high-risk human papillomavirus (hrHPV), abnormal cytology necessitates colposcopy and biopsy; however, cytology–histology concordance is variable and may differ by menopausal status. This study aimed to evaluate the concordance between cytologic findings and biopsy results in hrHPV-positive women with abnormal Pap tests and to compare outcomes by menopausal status. Materials and Methods: This retrospective, single-center study included 904 hrHPV-positive women with abnormal cytology who underwent colposcopy. Cytology findings [atypical squamous cells of undetermined significance (ASC-US), low-grade squamous intraepithelial lesion (LSIL), atypical squamous cells—cannot exclude high-grade squamous intraepithelial lesion (ASC-H), and high-grade squamous intraepithelial lesion (HSIL)] were compared with histological findings [normal, cervical intraepithelial neoplasia (CIN)-1, -2, -3]. Menopausal status was stratified as premenopausal (<48 years) and postmenopausal (≥48 years). Rates of cyto-histologic concordance, overestimation, and underestimation were calculated. Results: The predominant cytological result was ASC-US (61.7%), followed by LSIL (25.3%), whereas histologically, CIN was most common (66.5%; CIN-1: 42.8%, CIN-2: 11.5%, CIN-3: 12.2%). Cytology–biopsy concordance was 50.7%, with overestimation in 35.4% and underestimation in 13.9%. Overestimation was highest in ASC-US (43.9%) and ASC-H (37%), while underestimation was most frequently seen in LSIL cases (27.1%). HSIL cytology showed the highest agreement (85.7%). Conversely, LSIL cytology showed higher cyto-histologic concordance in postmenopausal women, whereas ASC-H and HSIL cytologies were more commonly overestimated in comparison to premenopausal women. Using ASC-H/HSIL as the positive cytology threshold for CIN-2+ detection, sensitivity was 41.1% and specificity was 95.8% [positive predictive value (PPV) 75.2%, negative predictive value (NPV) 84.0%; overall accuracy 82.9%]. The sensitivity and NPV were higher in postmenopausal women than in premenopausal women (50.0% vs. 39.9%; 91.3% vs. 82.3%, respectively). Conclusions: Cytology–histology concordance is moderate among women who are hrHPV-positive with abnormal cytology, characterized by notable underestimation in low-grade cytology and strong predictive value in HSIL cases. Menopausal status influences the outcomes; in postmenopausal women, high-grade lesions are less frequent, and diagnostic accuracy for detecting CIN-2+ is higher. These findings highlight the need for age- and menopause-sensitive diagnostic approaches.