Systemic onset juvenile idiopathic arthritis (SoJIA) is characterized by arthritis, fever and visceral organ involvement including hepatosplenomegaly, lympadenopathy and serositis. This is a case of SoJIA misdiagnosed as Kawasaki disease (KD) and developed machrophage activation syndrome (MAS) secondary to Ebstein-Barr virus (EBV) infection. It is presented to point out the conditions that may come along. First of all, SoJIA should be kept in mind while making the differential diagnosis of coronary arterial ectasias and dilatations usually seen in vasculitic diseases like KD. Second, as a very fatal complication MAS should always be considered while following a patient with the diagnosis of SoJIA. Infections like EBV may be the potential triggers for development of MAS especially in immunesupressed patients.