Objective: This study evaluated the performance of a flow cytometry system (LC-1000) in screening cervical precancerous lesions at routine health checkups. Study design: In total, 928 health examinees were enrolled at 16 health promotion centers in 13 Korean cities between 2016 and 2017. All participants underwent liquid-based cervical cytology and flow cytometry testing to determine the cell proliferation index (CPIx). Results: The positivity rate of the LC-1000 system increased with the severity of the cervical cytology findings (p for trend < 0.001). When low-grade squamous intraepithelial lesion (LSIL) or higher (including LSIL, high-grade squamous intraepithelial lesion [HSIL], and atypical squamous cells without excluding HSIL [ASC-H]) was defined as gold-standard positivity, the sensitivity, specificity, PPV, and NPV of LC-1000 were 75.3% (95% confidence interval [CI], 66.8–83.7), 58.5% (95% CI, 55.2–61.9), 18.1% (95% CI, 14.5–21.8), and 95.1% [95% CI, 93.2–97.0], respectively. The median CPIx increased significantly from normal cytology to HSIL (p < 0.001). The median CPIx was higher in high-risk human papillomavirus (HR-HPV)-positive cases than in HR-HPV-negative cases (0.23 vs. 0.17, p < 0.001), while it did not differ between HR-HPV-positive and HR-HPV-negative cases with normal cytology findings (0.16 vs. 0.16, p = 0.700). Conclusion: The LC-1000 system is potentially useful for screening cervical precancer and cancer, especially when excluding normal or ASC of undetermined significance cases in routinely screened populations.