Systemic juvenile idiopathic arthritis (SJIA) is a chronic arthritis of children characterized by a combination of arthritis and systemic inflammation. There is usually nonspecific laboratory evidence of inflammation at diagnosis but no diagnostic test. Normalized volumes from 89/889 2D protein spots representing 26 proteins revealed a plasma pattern that distinguishes SJIA flare from quiescence. Highly discriminating spots derived from 15 proteins constitute a robust SJIA flare signature and show specificity for SJIA flare in comparison to active polyarticular juvenile idiopathic arthritis (poly JIA) or acute febrile illness (FI). We used 7 available ELISA assays, including one to the complex of S100A8/S100A9, to measure levels of 8 of the15 proteins. Validating our DIGE results, this ELISA panel correctly classified independent SJIA flare samples, and distinguished them from acute febrile illness. Notably, data using the panel suggest its ability to improve on ESR or CRP or S100A8/S100A9, either alone or in combination in SJIA F/Q discriminations. Our results also support the panel’s potential clinical utility as a predictor of incipient flare (within 9 weeks) in SJIA subjects with clinically inactive disease. Pathway analyses of the 15 proteins in the SJIA flare versus quiescence signature corroborates growing evidence for a key role for IL-1 at disease flare.