Objectives: To describe human papillomavirus (HPV) vaccination practices in adolescent girls with systemic lupus erythematosus (SLE) and juvenile idiopathic arthritis (JIA) and to identify barriers to and motivators for vaccination. Methods: Cross-sectional, multicenter study on girls aged 9 to 19 years and their accompanying adults. The measurement criteria were the proportion of girls who were vaccinated against HPV, compliance with the vaccination schedule, factors associated with vaccination, and reasons for vaccination and non-vaccination through a self-administered questionnaire. Results: Seventy-one patients (16 with SLE and 55 with JIA) were included with a mean age of 13 years old (rank 11–18). According to parental questioning, 39% of patients were vaccinated against HPV or in progress (44% and 38% of SLE and JIA, respectively). This rate was 82% for the 22 patients ≥ 15 years of age. The vaccine was administered as often by a general practitioner (39%) as by a hospital pediatrician (also 39%). Two factors were significantly associated with vaccination: Older age (OR 53.68, 95% CI 5.85–429.29, p < 0.001) and previous hepatitis B vaccination (OR 4.97, 95% CI 1.03–24.01, p = 0.040). Recommendation of the vaccine by a health professional and fear of HPV-related diseases were the main facilitators. Lack of knowledge about the vaccine, lack of recommendation by a health professional, and fear of vaccine side effects were the main barriers. Conclusions: HPV vaccination coverage remains insufficient among patients with autoimmune disease. Education and awareness of health professionals about HPV infections are crucial elements in vaccine acceptance.