For neonates with right atrial isomerism (RAI), functional single ventricle (f-SV), and obstructive total anomalous pulmonary venous connection (TAPVC), primary TAPVC repair (TAPVCR) has a poor outcome. At our hospital, the survival rate at 1 year of such neonates undergoing primary TAPVCR between 1999 and 2010 (TAPVCR group) was 30% (3/10). Most deceased cases suffered from capillary leak syndrome and unstable pulmonary resistance after the surgeries. We sought to determine whether less invasive primary draining vein stenting (DVS) improved the outcome of these neonates. We investigated outcomes in consecutive nine such neonates (median gestational age 38 weeks, birth weight 2.8 kg, females 4) who underwent primary DVS with 6-mm-diameter Palmaz® Genesis® stents at our hospital between 2007 and 2017 (DVS group). Eight patients underwent subsequent surgeries to adjust the pulmonary flow after decreased pulmonary resistance. The survival rate at 1 year after the first interventions in the DVS group improved to 77% (7/9), although there was a difference between the interventional eras of the two groups. Of the seven patients who underwent multiple stent redilations with a larger balloon or additional stenting in other sites until the next stage of surgery at a median age of 8 months, four received a bidirectional Glenn (BDG) shunt and TAPVCR and three underwent TAPVCR, with two of those cases reaching BDG. Less invasive primary DVS improved the outcome of neonates with RAI, f-SV, and obstructive TAPVC, with many reaching BDG. Patient selection to advance toward Fontan is thought to further improve the outcome.