Kawasaki disease (KD) is an acute, self-limited vasculitis that predominantly affects children under five years and can lead to coronary artery aneurysms. Incomplete KD involves an incomplete clinical picture supported by echocardiographic and laboratory findings. In this case, a six-month-old male child presented with a two-day fever, maculopapular erythematous rash, nonpurulent conjunctivitis, throat congestion, mild cough, intermittent loose stools, and was initially diagnosed with a viral illness treated symptomatically. Three days later, he re-presented with unresolved symptoms. Laboratory findings showed significantly elevated inflammatory markers, leukocytosis, and thrombocytosis. Chest X-ray was normal, and IgM measles test, respiratory viral panel, and mycoplasma serology were negative. The fever was managed with antipyretics and intravenous antibiotics, and antibiotic eye drops were given for the conjunctivitis. He improved clinically and repeat investigations showed improvement, following which he was discharged on oral antibiotics and antibiotic eye drops. Three days later (day 10 of illness), he presented with high spiking fever for 48 hours, bilateral nonpurulent conjunctivitis, and exudative tonsillitis. After excluding viral or bacterial etiologies, the patient was further evaluated for KD. Echocardiogram showed dilated coronary arteries, including an evolving aneurysm in the left anterior descending artery, confirming incomplete KD. He was treated with intravenous immunoglobulin and aspirin, leading to the resolution of his symptoms within 24 hours. Follow-up echocardiogram showed improvement and he was discharged on aspirin with scheduled cardiac monitoring. This case highlights the diagnostic challenges of incomplete KD, its potential association with underlying infections, and the effectiveness of timely treatment.