Intramural coronary artery is known to be a risk factor for early death after an arterial switch operation (ASO). We evaluated the early and mid-term results of ASO for patients with intramural coronary artery. From September 2008 to March 2012, seven patients with an intramural coronary artery underwent ASO at our hospital. The mean age at operation was 2.4 months (2 days–1 year), and the mean body weight was 4.3 ± 2.2 kg. The mean follow-up was 35.3 ± 16.5 months (22–63 months). The individual coronary button technique was used in seven patients. The intramural segment was unroofed in one patient; in one patient with myocardial ischemia, the intramural segment was unroofed and enlarged using a patch of autologous pericardium. There was one operative death because of low cardiac output syndrome (14.2 % mortality). In the same time period at our hospital, three deaths were reported in 68 ASO patients (4.4 % mortality) without an intramural coronary artery. There was no statistical difference between the two groups (P > 0.05). There were no late deaths, and no patients required a coronary intervention. Intramural coronary artery is a well-known risk factor for early death after ASO. To optimize results, the coronary transfer technique should be tailored to each patient’s particular anatomy. Intraoperative or postoperative myocardial ischemia should be addressed aggressively by immediately reimplanting the coronary artery. Unroofing the intramural segment, even the distal portion, should restore normal coronary blood flow.