Objective To investigate the clinical features and long-term prognosis of systemic juvenile idiopathic arthritis (sJIA) complicated with macrophage activation syndrome (MAS). Methods The clinical data of sJIA children complicated with MAS treated from August 2014 to August 2020 were retrospectively analyzed. The sJIA children without MAS diagnosed and treated in the same period were classified as sJIA without MAS group. The clinical manifestations and long-term prognosis were compared between the two groups. Results The median onset age of the 25 patients (11 boys and 14 girls) in sJIA with MAS group was 5.8 (2.6-10.0) years. The median onset age of 38 patients (18 boys and 20 girls) in sJIA without MAS group was 7.0 (5.1-9.0) years. Twenty-one patients had MAS in the early stage of sJIA. Compared with the sJIA without MAS group, the incidence of hepatosplenomegaly, respiratory system involvement, central nervous system involvement and bleeding in the sJIA with MAS group was higher, and the difference was statistically significant (P<0.05). Methemoglobinemia was the most common abnormal laboratory index in sJIA patients with MAS (100%), followed by elevated aspartate aminotransferase (24 cases) and decreased fibrinogen (23 cases). All patients were treated with glucocorticoids, 22 with intravenous immunoglobulin and 22 with cyclosporin A. Tocilizumab was added to 11 patients, 4 of them were treated with tocilizumab within 2 to 3 weeks of MAS activity, and 7 were treated with tocilizumab when sJIA was still in an unstable state after MAS remission. The median follow-up time was 40.0 (26.5-60.5) months. The results of follow-up to August 31, 2022 showed that there were 11 cases of monophasic course, 5 cases of recurrent course, and 9 cases of persistent course in the sJIA with MAS group, and there was no statistically significant difference in long-term prognosis compared with the sJIA without MAS group (P>0.05). Growth retardation occurred in 4 sJIA children with MAS who received glucocorticoid therapy for a long duration. Hormonal cataract occurred in 3 sJIA children with MAS. Conclusions For sJIA children complicated with MAS, if early identification, effective treatment and standardized management can be given in time, the long-term prognosis is similar to that of children without MAS.