In pediatric care, the range of potential diagnoses for arthritis can be relatively extensive, primarily involving infectious and inflammatory causes and, to a lesser extent, oncological conditions. Specifically, when addressing inflammatory causes, differentiating between Juvenile Idiopathic Arthritis (JIA) and Reactive Arthritis (ReA) can prove to be challenging during the first weeks, owing to the lack of specific antibodies in several JIA subtypes. This single-center retrospective study of 108 children with arthritis aimed to evaluate in greater detail the complete blood count (CBC) profiles of children with JIA and ReA in greater detail. The most significant differences were noted in terms of the Systemic Immune-Inflammation Index (SII), with higher values in the JIA group. Moreover, within the JIA group, SII displayed a significant positive correlation with conventional inflammatory biomarkers, specifically C-reactive protein (ρ = 0.579) and Erythrocyte Sedimentation Rate (ρ = 0.430). It was the only independent factor associated with the presence of JIA after adjusting for age (p = 0.030). Also, even with the moderate diagnostic value, the discriminating capacity of SII was superior to those of each of its component CBC parameters according to receiver operating characteristic (ROC) analysis. In summary, this study identified elevated SII values in the JIA group compared to the ReA group, indicating the potential utility of SII as an adjuvant discriminatory marker between these two arthritis forms.