While cluster headaches are classified and considered a primary headache disorder, secondary causes of cluster headaches have been reported and may provide insight into cluster headaches' potential pathophysiology. The mechanisms underlying this headache phenotype are poorly understood, and several theories have been proposed that range from the activation within the posterior hypothalamus to autonomic tone dysfunction. We provide a review of reported cases in the literature describing secondary causes after cardiac procedures. We will present a novel pediatric case report of a 16-year-old boy with an isolated innominate artery who presented with acute new-onset headaches 8 h following cardiac catheterization of the aortic arch with arteriography and left pulmonary artery stent placement. The headaches were characterized by attacks of excruciating pain behind the left eye and jaw associated with ipsilateral photophobia, conjunctival injection, rhinorrhea, with severe agitation and restlessness. These met the International Classification of Headache Disorders-3 criteria for episodic cluster headaches. The headaches failed to respond to non-steroidal anti-inflammatory medications, dopamine antagonists, and steroids. He showed an immediate response to treatment with oxygen. This unique case of cluster headaches following cardiac catheterization in a pediatric patient with an isolated innominate artery may provide new insight into cluster headaches' pathogenesis. We hypothesize that the cardiac catheterization induced cardiac autonomic changes that contributed to the development of his cluster headaches. The role of aortic arch anomalies and procedures in potential disruption of the autonomic tone and the causation of cluster headaches is an area requiring further study.