Objectives: Vaccination of systemic lupus erythematosus patients with non-live vaccines may decrease vaccine-preventable infections and mortalities. In the present study, we aimed to compare the immunogenicity and safety of inactivated hepatitis A vaccination in childhood-onset systemic lupus erythematosus and healthy subjects. Methods: A total of 30 childhood-onset systemic lupus erythematosus and 39 healthy participants who were seronegative for hepatitis A received two doses of the hepatitis A vaccine in a 0- and 6-month schedule. Hepatitis A virus (HAV) IgG antibodies were measured before vaccination and 7 months after the vaccination. Results: Although anti-HAV IgG antibody titers after vaccination were found to be somewhat lower in children with systemic lupus erythematosus than that of the healthy subjects (p < 0.05), the difference in seroconversion rate was insignificant between childhood-onset systemic lupus erythematosus patients (n = 24/30, 80%) and healthy controls (n = 33/39, 84.6%). There was no increase in median Systemic Lupus Erythematosus Disease Activity Index (SLEDAI)-2K scores and anti-ds DNA levels after the vaccination procedure. Seroconversion rates in childhood-onset systemic lupus erythematosus patients were not affected by medication, high disease activity (SLEDAI-2K >6) and anti-ds DNA positivity. None of the patients experienced any flare or adverse reaction throughout the study. Conclusions: According to these results, we conclude that inactivated hepatitis A vaccine is safe and well tolerated in childhood-onset systemic lupus erythematosus patients, with no adverse events or increase in activity. Immunogenicity to the hepatitis A vaccine was adequate, with a seropositivity rate of 80%.