Background <p>Human Papillomavirus (HPV) E6/E7 mRNA testing has been proposed as a potential improvement over HPV DNA testing for predicting cervical lesion progression. This systematic review and meta-analysis evaluated the diagnostic performance of HPV E6/E7 mRNA testing across various clinical scenarios.</p> Methods <p>A comprehensive search was conducted in Medline, Embase, Cochrane, Web of Science, and other databases. Two clinical scenarios were analyzed: triage of atypical squamous cells of undetermined significance (ASCUS), prediction of post-conization recurrence.. Diagnostic accuracy was assessed using standardized quality appraisal tools, with results synthesized through forest plots and Summary Receiver Operating Characteristic (SROC) curves.</p> Results <p>In ASCUS triage, all mRNA methods, including PreTect, APTIMA, and QuantiVirus, achieved comparable sensitivity but significantly higher specificity than DNA testing, with PreTect showing the strongest performance. For post-conization recurrence prediction, QuantiVirus and PreTect assays provided similar sensitivity but greater specificity compared to HPV DNA testing.</p> Conclusion <p>HPV E6/E7 mRNA testing offers higher specificity while maintaining comparable sensitivity to HPV DNA testing across multiple clinical scenarios. For ASCUS triage, PreTect demonstrates superior performance with the highest specificity and should be prioritized for clinical implementation in this setting. For post-conization recurrence prediction, QuantiVirus provides optimal diagnostic accuracy and represents the preferred choice for surveillance following cervical conization.</p> Systematic review registration <p>PROSPERO: CRD42023473415.</p>