We aimed to validate the reliability of the Medical Outcomes Study Short Form-36 (SF-36) among Japanese patients with systemic lupus erythematosus (SLE). Japanese patients with SLE (n = 233) completed the SF-36 and other related demographic questionnaires, and physicians simultaneously completed the SLE Disease Activity Index 2000 (SLEDAI-2K) and the Systemic Lupus International Collaborating Clinics Damage Index (SDI). Patients were prospectively followed for a repeat assessment the following year. The SF-36 subscales demonstrated acceptable internal consistency (Cronbach’s α of 0.85–0.89), and an overall good test–retest reliability (intraclass correlation coefficient >0.70). The average baseline SF-36 subscale/summary scores except for “bodily pain” were significantly lower than those of the Japanese general population (p < 0.05). The SDI showed an inverse correlation with the SF-36 subscale/summary scores except for “vitality” and “mental component summary” at baseline, whereas the SLEDAI-2K did not. In the second year, “social functioning” and “mental component summary” of the SF-36 deteriorated among patients whose SDI or SLEDAI-2K score increased (effect sizes < −0.20). In conclusion, the SF-36 demonstrated acceptable reliability among Japanese patients with SLE. Health-related quality of life measured by the SF-36 was reduced in Japanese patients with SLE and associated with disease damage, rather than disease activity.