As a major organ dysfunction, some patients with Kawasaki disease (KD) present with hypotension or shock, known as KD shock syndrome (KDSS). Organ dysfunction is also seen in macrophage activation syndrome (MAS), complicating KD (MAS-KD). Both KDSS and MAS are rare but potentially life-threatening complications of KD that require early recognition. In practice, however, KDSS and MAS can sometimes be overlooked in patients with KD. Here, we describe a 13-year-old boy who presented with prolonged fever, rash, and red eyes, and subsequently developed hypotension. He was diagnosed with KDSS and received inotropic agents and intravenous immunoglobulin (IVIG) treatment. However, his clinical and laboratory features deteriorated, and he met the diagnostic criteria for MAS. KDSS and MAS-KD share many overlapping features in terms of organ dysfunction. A diagnosis of KDSS is made when a patient with KD shows cardiac dysfunction, such as shock. If a KD patient displays multi-organ dysfunction, such as hematologic, hepatic, renal, or neurologic symptoms, they should be diagnosed with MAS-KD. As demonstrated in this case report, some KD patients may present with both cardiac and multi-organ dysfunction and require prompt and proper treatment for both.