Introduction: Access to patient medical data is critical to building a real-time data analytic pipeline for improving care providers’ ability to detect, diagnose, and prognosticate diseases. Critical congenital heart disease (CCHD) is a common group of neonatal life-threatening defects that must be promptly diagnosed to minimize morbidity and mortality. CCHD can be diagnosed both prenatally and postnatally. However, despite current screening practices involving oxygen saturation analysis, timely diagnosis is missed in approximately 900 infants with CCHD annually in the USA and can benefit from increased data processing capabilities. Adding non-invasive perfusion measurements to oxygen saturation data can improve the timeliness and fidelity of CCHD diagnostics. However, real-time monitoring and interpretation of non-invasive perfusion data are currently limited. Methods: To address this challenge, we created a hardware and software architecture utilizing a Pi-top™ for collecting, visualizing, and storing dual oxygen saturation, perfusion indices, and photoplethysmography data. Data aggregation in our system is automated and all data files are coded with unique study identifiers to facilitate research purposes. Results: Using this system, we have collected data from 190 neonates, 130 presumably without and 60 with congenital heart disease, in total comprising 1665 min of information. From these data, we are able to extract non-invasive perfusion features such as perfusion index, radiofemoral delay, and slope of systolic rise or diastolic fall. Conclusion: This data collection and waveform analysis is relatively inexpensive and can be used to enhance future CCHD screening algorithms.