Background Previous studies showed conflicting results regarding the association between systemic lupus erythematosus (SLE) and risk of cervical atypia. Therefore, the present study aimed to make a meta-analysis to summarize results of studies regarding association between SLE and risk of cervical atypia. Methods We searched for articles published before March 2021 in in the following databases: PubMed, EMBASE, Web of Science, Medline and Google Scholar. Odds ratios (ORs) and relative risks (RRs) with their 95% confidence intervals (CIs) were computed to create a pooled effect size and 95% CI using STATA 12.0 software. Results The present meta-analysis showed that SLE was significantly associated with increased risks of cervical atypia (OR/RR = 2.94, 95% CI 2.22 to 3.89, I2 = 92.1%, p < .001), cervical cancer (OR/RR = 3.13, 95% CI 2.09 to 4.70, I2 = 84.7%, p < .001), squamous intraepithelial lesion (SIL) (OR/RR = 5.00, 95% CI 2.58 to 9.69, I2 = 88.9%, p < .001) and low-grade SIL (OR/RR = 3.14, 95% CI 1.29 to 7.67, I2 = 63.3%, p = .018) with random effects models. Conclusion In summary, findings of this meta-analysis demonstrated that SLE was associated with a higher risk of cervical pre-malignant lesions and carcinoma. It may be necessary for clinicians to remind women with SLE to screen human papillomavirus infection and be vaccinated as soon as possible. However, caution is required when interpreting our findings. Further studies, especially well-designed randomized controlled clinical trials are awaited to confirm the association between SLE and cervical atypia–associated diseases.