There is less certainty regarding the best strategy for treating neonates with functional single ventricle (SV) and hypoplastic aortic arch. We have applied a modified extended aortic arch anastomosis (EAAA) and main pulmonary artery banding (PAB) as an initial palliation in neonates with transverse arch hypoplasia and assessed the mid-term outcomes. In total, 10 neonates with functional SV and extensive hypoplasia or interruption of the arch underwent a modified EAAA (extended arch anastomosis with a subclavian flap) concomitant with main PAB through a thoracotomy without cardiopulmonary bypass. Patient age and weight ranged from 4 to 14 days and 2.3 to 3.8 kg, respectively. There were no hospital deaths although there were two late deaths. Gradients across the arch were 0 to 7 mmHg at postoperative day 1 and no arch reoperations were required. Two patients required balloon aortoplasty. Nine underwent bidirectional cavopulmonary shunt and two of them needed concomitant Damus-Kaye-Stansel (DKS) anastomosis. Six have completed Fontan. Our modification of EAAA with main PAB for SV neonates may benefit a certain population with transverse arch hypoplasia as an option to be considered. Patients with the potential for developing outflow obstruction may be best managed with an initial DKS-type palliation.