The complement system plays a role in the pathogenesis of some autoimmunopathies. This longitudinal study evaluates the contribution of the complement system in the pathogenesis of oligoarticular juvenile idiopathic arthritis (JIA). Serum of the peripheral blood and the synovial fluid were investigated for the activity of the classical (CP), the mannose binding lectin (MBL), and the alternative pathway (AP). A total of 12 samples from peripheral blood (PB) and two samples from synovial fluid (SF) of girls with oligoarticular JIA were investigated in a longitudinal observation from the time point of the diagnosis of JIA. The differences between the complement activity in the PB and in the SF were extremely statistically significant (CP and MBL: P < 0.0001; AP: < 0.0087). The activity of the CP and the MBL pathway was reduced. The AP is the main contributor in the pathogenesis of oligoarticular JIA. Anti-C5 therapy may be an option to avoid the creation of the membrane attack complex.