Accurate early detection of breast and cervical cancer is vital for treatment success. Here, we conduct a meta-analysis to assess the diagnostic performance of deep learning (DL) algorithms for early breast and cervical cancer identification. Four subgroups are also investigated: cancer type (breast or cervical), validation type (internal or external), imaging modalities (mammography, ultrasound, cytology, or colposcopy), and DL algorithms versus clinicians. Thirty-five studies are deemed eligible for systematic review, 20 of which are meta-analyzed, with a pooled sensitivity of 88% (95% CI 85–90%), specificity of 84% (79–87%), and AUC of 0.92 (0.90–0.94). Acceptable diagnostic performance with analogous DL algorithms was highlighted across all subgroups. Therefore, DL algorithms could be useful for detecting breast and cervical cancer using medical imaging, having equivalent performance to human clinicians. However, this tentative assertion is based on studies with relatively poor designs and reporting, which likely caused bias and overestimated algorithm performance. Evidence-based, standardized guidelines around study methods and reporting are required to improve the quality of DL research.