Introduction: The mortality and morbidity of meconium aspiration syndrome in neonates born with meconium-stained amniotic fluid in developing countries are still high. In Nepal, few studies have estimated the prevalence of meconium-stained amniotic fluid among newborns. The study aimed to find out the prevalence of neonates born through meconium-stained amniotic fluid among deliveries in a tertiary care centre. Methods: This descriptive cross-sectional study was conducted among neonates born in a tertiary care centre from November 2021 to March 2022. Neonates born during the study period with meconium-stained amniotic fluid were studied. Ethical approval was obtained from the Institutional Review Committee. Convenience sampling method was used. With permission from the Department of the Neonatal Intensive Care Unit, the data were collected and entered in a Microsoft Excel sheet. Point estimate and 95% Confidence Interval were calculated. Results: Among 576 neonates, the prevalence of neonates born through meconium-stained amniotic fluid was 77 (13.37%) (10.59-16.15, 95% Confidence Interval). Conclusions: The prevalence of neonates born through meconium-stained amniotic fluid was found to be similar to other studies done in similar settings.