We present a case report of a patient diagnosed with Holt-Oram syndrome (HOS) presenting with clinical and electrophysiologically confirmed carpal tunnel syndrome. Pre-operative Magnetic resonance imaging revealed an abnormal course of the median nerve; as such an atypical incision and approach were carried out to decompress the nerve to excellent post operative clinical effect. To our knowledge this is the first description of abnormal nervous course in a patient with HOS leading to peripheral entrapment. A literature surrounding the important aspects of HOS to the orthopaedic surgeon is presented concomitantly.