Objective: To describe the observational findings of functional echocardiography (FnEcho) in neonatal intensive care unit of a tertiary care hospital by evaluating its frequency of use, characteristics of patients and distribution of heart diseases. Methodology: This Prospective descriptive observational study was done in a tertiary neonatal intensive care unit (NICU) in Rawalpindi, from July 2017 to June 2018. A total of two hundred and twelve neonates admitted to the NICU undergoing echocardiographic assessment were included in the study. Qualitative variables like gender, mode of delivery, and diagnostic findings were represented in terms of frequency and percentages. Quantitative data like age, birth weight and gestational age were highlighted as mean and standard deviation. Results: Out of a total of 212 neonates, 111 (52.4%) were male. The mode of delivery was noted to be lower segment cesarean section among 126 (60.0%) neonates. The mean gestational age was found to be 36.47+2.3 weeks, ranging from 28 to 41 weeks, whereas the mean birth weight was 2.56+0.68 kg, ranging from 1.1 to 4.2 kg. A total of 75 neonates were found to have functional heart disease in the form of pulmonary hypertension 37 (17.4%), hemodynamically significant patent ductus arteriosus 24(11.3%), hypoxic ischemic cardiomyopathy 4(1.9%), and systemic hypotension 10 (17.4%). Conclusion: FnEcho was found to be an effective tool for identifying different kinds of functional and structural heart defects. VSD was found to be the most common type of congenital heart disease, followed by PDA. Timely intervention in PPHN was also rewarding with good outcome.