Background: Septic arthritis in children is a joint threatening condition with potentially severe consequences; however, long-term outcome data is lacking. This study aims to determine 1-20-year outcomes following septic arthritis of hip and knee joints in children in an Australian population. Methods: All paediatric patients with septic arthritis of the hip or knee from 1995 to 2015 treated at our Australian institution were retrospectively assessed. Clinical features, treatment and investigation results were recorded. Long-term functional and radiological outcomes, infection recurrence and reoperation rate at final follow-up (mean 8.5 years, range 1.0-20.3; hip versus mean 7.7 years, range 1.1-20.3; knee) were recorded. Results: Sixty-four patients (37 hip, 27 knee) met inclusion criteria. Fifty-two patients (81.3%) attended follow-up. No mortalities or late infection recurrence occurred. Three patients (1; hip versus 2; knee) had a later operation. Median Oxford scores were excellent (48; hip versus 48; knee); however, a significant proportion had a degree of impaired function (31.3%; hip versus 42.1%; knee). Radiological outcomes were excellent in knees more commonly than hips (81.3%; hip versus 100%; knee). Conclusions: Outcomes at 1-20 years for the majority of patients following septic arthritis of the hip and knee are excellent with early joint irrigation and intravenous antibiotics. Our results demonstrate a significant proportion of patients following septic hip arthritis have mild to moderately poor functional and radiological outcomes. Those with septic knee arthritis demonstrated universally excellent radiological outcomes and mild functional impairment in approximately one-third of cases.