Cervical cancer, the second most common cancer affecting women in Northern Brazil, is strongly associated with human papillomavirus (HPV) infection. Diseases affecting the immune state of a patient, including autoimmune diseases like systemic lupus erythematosus (SLE), can lead to persistent HPV infection and cancer. We evaluated cervical HPV prevalence and the associated risk factors in 70 women with SLE in the city of Belém, located in Brazilian Amazon. HPV DNA was detected by PCR using primers MY9 and MY11. HPV subtypes were determined by real-time PCR, using specific probes. Overall, prevalence of cervical HPV in women with SLE was 22.8%. HPV prevalence was significantly higher in younger women (aged 18–25 years; 75%, p< 0.0001), in women who had not given birth (50%, p = 0.01), and in women with no prior pregnancy (57%, p = 0.003). Five women (7.1%) had Pap smears with a cytopathological outcome suggestive of HPV; four of these women were HPV-positive. No women with both, SLE and HPV, had a normal Pap smear. Of the women diagnosed with SLE in the last 1–5 years, 75% was HPV-positive (p = 0.04). The two most prevalent HPV subtypes were HPV 58 (37.5%) and HPV 31 (31.3%). These results are important for understanding HPV infection in women with SLE and are valuable tools for developing cervical cancer prevention strategies and health management policies.