Background: Kawasaki Disease (KD) is an acute vasculitis affecting children under five years of age, with atypical presentations posing diagnostic challenges and a higher risk of coronary complications when untreated. Methods: We report on a 2-year-old girl with persistent fever, limb edema, erythema, and non-purulent conjunctivitis, without cervical lymphadenopathy or the typical rash. Inflammatory markers were assessed, and a cytokine expression profile was obtained using qRT-PCR. Results: Laboratory analysis showed elevated C-reactive protein (11.1 mg/dL), high fibrinogen (468 mg/dL), borderline D-dimer (484 ng/mL), and a normal platelet count. The cytokine profile revealed marked upregulation of IFN-α, IFN-β, IFN-γ, IL-1α, IL-1β, IL-5, IL-8, and IL-12, with downregulation of IL-2 and IL-4, as well as low TNF-α levels. These findings, although not pathognomonic, were consistent with an inflammatory profile compatible with atypical KD, in which a preceding viral infection may have played a role, although causality cannot be established. Conclusions: This case highlights the diagnostic utility of cytokine profiling in suspected atypical KD, particularly when clinical criteria are incomplete. The integration of immunological data may aid in earlier recognition and therapeutic intervention, thereby helping to prevent cardiovascular sequelae. Cytokine analysis may serve as a promising adjunct for atypical KD diagnosis, although confirmation in larger cohorts is needed.