One possible cause of Harlequin syndrome is a lesion to the preganglionic or postganglionic cervical sympathetic fibers and parasympathetic neurons of the ciliary ganglion. It is also believed that torsion (twisting) of the thoracic spine can cause blockage of the anterior radicular artery leading to Harlequin syndrome. The sympathetic deficit on the denervated side causes the flushing of the opposite side to appear more pronounced. It is unclear whether or not the response of the undamaged side was normal or excessive, but it is believed that it could be a result of the body attempting to compensate for the damaged side and maintain homeostasis.

Since the cause and mechanism of Harlequin syndrome is still unknown, there is no way to prevent this syndrome.

Although the exact mechanism for Harlequin syndrome is still unclear, understanding what is affected with this syndrome is important. Majority of cases are thought to occur when nerve bundles in the head and neck are injured. Such bundles are able to send an action potential from the autonomic nervous system to the rest of the body. However, action potentials in this system are not being received by the second or third thoracic vertebrae which innervates the face, neck, and upper chest. Damage or lesions near T2 or T3 could be between the stellate ganglion and superior cervical ganglion. This is where we would observe absence of sweat and skin flushing on one side of the face, neck, and upper chest. Harlequin Syndrome may be classified as the following: Primary, Idiopathic, Congenital, Secondary, Organic lesion, Iatrogenic cause.