Background: Neonatal jaundice is a common condition especially in the first week of life. There are various maternal and neonatal clinical characteristics that have been associated with pathological jaundice. Objectives: To describe clinical profile of pathological jaundice and to estimate its prevalence among newborns admitted at the National Referral Hospital. Methods: A cross-sectional descriptive study design was used to study pathological jaundice cases admitted at the Gyaltsuen Jetsun Pema Neonatal Intensive Care Unit (NICU) of Jigme Dorji Wangchuck National Referral Hospital (JDWNRH) from 7th November 2018 till 6th November 2019. Data was collected using a predesigned case proforma, entered and analyzed in Epidata after obtaining ethical clearance from the Research Ethics Board of Health (REBH), Bhutan.  Results: Facility based prevalence rate of pathological neonatal jaundice was found to be 63.66% in our setting. The median age on presentation was 4 days. Blood group ABO incompatibility and neonates less than one week of age were found to be most common neonatal profile in this study. Significant association was found between primiparous mothers and excessive weight loss. Conclusion: The prevalence of pathological jaundice was high in our setting. ABO incompatibility, neonates less than one week of age, primigravida mothers with feeding issues should be closely followed or screened for pathological jaundice especially during the first one week of life. Keywords: Pathological jaundice, Prevalence, ABO incompatibility, feeding issues, excessive weight loss