Our objective was to investigate the pattern of damage accumulation in patients with juvenile-onset systemic lupus erythematosus (JSLE) and the relationship between damage accrual, disease flares and cumulative drug therapies. All patients with SLE followed prospectively in three tertiary care centres were identified. Only patients who presented within 12 months of diagnosis and were followed for at least three years were included. Damage was measures based on chart review using the SLICC/ACR damage index (SDI), which was modified (M-SDI) by adding the item growth failure. Mild-moderate and severe disease flares were defined by the increase in SLEDAI-2K. The cumulative duration of drug therapies was calculated in each patient. Fifty-seven patients were included. The mean M-SDI score for the whole patient group increased over time, from 0.1 at one year to 0.8 at three years to 1.5 at five years. Ocular and renal damage and growth failure were observed most frequently. Compared to patients with stable damage, patients who accrued new damage had a significantly greater frequency of severe disease flare in the first three years of follow-up. No significant difference was observed in any cumulative drug therapy between patients who accrued damage and those who did not. Damage accrual was associated with severe disease flares, suggesting that judicious use of immunosuppressive agents to achieve prompt control of severe exacerbation of disease activity is important in minimizing damage in patients with JSLE.