Background Several recent studies have shown improved short-term outcome of steroid-resistant nephrotic syndrome (SRNS) in children; however, only a few studies have evaluated the long-term outcome. The aims of our study were to obtain detailed data and analyze the long-term outcome of children with SRNS. Methods Sixty-nine children with idiopathic SRNS were enrolled and divided into two groups based on initial histopathological patterns: focal segmental glomerulosclerosis (FSGS) and minimal change (MC)/diffuse mesangial proliferation (DMP). The effects of initial treatment with the immunosuppressant of choice (cyclosporine or cyclophosphamide) on renal survival, remission, and incidence of complications were analyzed in both groups (4 subgroups). Results The renal survival rate was significantly different among the four different subgroups based on different combinations of initial histopathological pattern (FSGS vs. MC/DMP) and initial immunosuppressant used for treating SRNS (cyclosporine vs. cyclophosphamide) ( P  = 0.013), with renal survival in the FSGS (cyclophosphamide) subgroup being especially low (54.6 %). Disease- and/or treatment-associated complications were relatively low; however, hypertension at last examination was observed in a considerable number of patients (31.9 %). Conclusions Our results suggest that a recently developed therapeutic regimen with cyclosporine considerably improves both the initial remission rate and the long-term renal survival rate of children with idiopathic SRNS.