Background The rate of glucocorticoid (GC) use is significantly higher in systemic juvenile idiopathic arthritis (SJIA) than other juvenile idiopathic arthritis subtypes. There is no consensus on the duration and dosage of GC treatment. We aimed to investigate the risk factors for a polyphasic / persistent disease course and the effect of dose and duration of GC treatment on SJIA prognosis. Methods Forty-two patients who were diagnosed with SJIA, and for whom the duration of disease was longer than 2 years, were included. Patients were divided into monophasic and others (polyphasic / persistent disease course). Risk factors for polyphasic / persistent disease course, which were clinical and laboratory findings regarding the patients, treatment options, dose, and duration of GCs, were evaluated for the first active disease periods and for all flares in the entire disease course. Results Of the 42 SJIA patients, 21 had monophasic, and 21 had polyphasic / persistent disease. Cumulative dosages and durations of glucocorticoid treatment were similar in the two groups at the first flare (odds ratio (OR): 1.032 P: 0.671; OR:1,113 P: 0.115). Durations of the first active disease period were longer in the polyphasic / persistent group (OR:1.275, P: 0.01). Active disease duration cut-off values of 1.5 months with sensitivity 85.7%, specificity 52.4% were observed on receiver operating characteristic curve analysis. The presence of hepatosplenomegaly at first flare was detected as an independent risk factor of polyphasic/persistent disease by multivariate analysis included both dosage and duration of a steroid (hazard ratio (HR): 4.129, P: 0.034), (HR: 3.992, P: 0.038). Multivariate recurrent events survival analysis determined ALT levels as a risk factor affecting polyphasic / persistent disease (HR: 0.986, P: 0.037). Conclusions Glucocorticoid dose and duration did not affect the active disease periods and disease course in SJIA. An active disease period longer than 1.5 months, presentation of hepatosplenomegaly at the initial disease course, and high ALT levels at the recurrences should warn physicians of polyphasic / persistent disease.