Background Almost eight children per 1000 live births are expected to have a congenital heart defect globally. The seven most critical congenital heart conditions that cause severe compromise on the patient’s quality and duration of life are collectively referred to as the Critical Congenital Heart Diseases (CCHD). CCHD is a critical condition that requires prompt detection and intervention as a life-saving measure. Pulse oximetry is a non-invasive, highly specific, and moderately sensitive method that can be used for screening new-borns for CCHD. The Emirates Health Services (EHS), UAE, adopted a strategy of developing a stringent program for newborn screening of Critical Congenital Heart disease, which would help in the early diagnosis and treatment of CCHD patients. An automated EMR (Wareed) driven solution was introduced to enhance this program as part of the routine workflow for the nurse care providers. Methods Our study is a retrospective observational study that aims to understand: the prevalence of CCHD in our target population and to study the impact of an automated program on screening compliance and its implications for early diagnosis of CCHD. Results We found that an EMR-driven automated screening program was highly effective in achieving high compliance (98.9%). It created a (statistically significant) improvement in the disease identification for CCHD in live births at EHS facilities. Conclusion We conclude that implementing an automated protocol through the EMR can effectively improve new-born screening coverage. It reduces the days to CCHD diagnosis, which would improve health outcomes in neonates.