This study evaluates the effectiveness of mandatory pulse oximetry screening. The objective is to evaluate whether mandatory pulse oximetry testing had decreased the late critical congenital heart disease (CCHD) diagnosis rate and reduced mortality in neonatal subjects. This was a single center, retrospective cohort study comparing the timing of diagnosis of CCHD between neonates undergoing cardiac surgery in 2009–2010, prior to mandatory pulse oximetry screening, and neonates in 2015–2016, after mandatory pulse oximetry screening was instituted. Follow-up was for 1 year. We defined CCHD as lesions requiring surgical correction within 30 days of life. Exclusions included: pacemaker insertions, vascular ring divisions, closure of patent ductus arteriosus, arterial cutdown, or extracorporeal membrane oxygenation cannulation without structural heart disease as the sole procedure, or if subjects were born at home. Infants diagnosed prior to discharge from birth hospital were defined as early postnatal; late postnatal subjects were diagnosed after birth hospital discharge. In-hospital mortality and 1-year mortality were measured. A total of 527 neonates were included; 251 (47.6%) comprised the pre-mandatory pulse oximetry screening cohort (2009–2010). Only 3.6% of the 2009–2010 cohort and 4.3% of the 2015–2016 cohort were diagnosed late (p = 0.66). One-year mortality decreased during the study period (17.2% in 2009–2010 vs 10.5% in 2015–2016, p = 0.03). There were no deaths in the late CCHD diagnosis groups. Mandatory pulse oximetry screening legislation has not changed the late postnatal diagnosis rate at our institution. Mortality for neonatal CCHD has declined, but this decline is not attributable to mandatory pulse oximetry screening.