Background In vitro fertilisation (IVF) offers a solution for infertility but poses increased obstetrical and perinatal risks, including higher rates of preterm birth, low birth weight and congenital anomalies. Particularly, IVF-related multiple pregnancies face significantly higher risks for preterm birth and prolonged hospital stays. This study compares neonatal outcomes between IVF and natural conception, as well as between singleton and IVF-related multiple pregnancies over the past decade. Method This retrospective study reviewed the medical records of babies born at Cipto Mangunkusumo Kencana Hospital from 2013 to 2023. Neonatal morbidities (hypothermia, hypoglycaemia, respiratory distress, circulation problems, sepsis, congenital anomalies, all stages of intraventricular haemorrhage and retinopathy of prematurity of all babies, neonatal intensive care unit (NICU) admission and length of stay) were dependent variables, with the mode of conception as the independent variable. Result Of 609 subjects, 169 were IVF conceptions and 435 natural conceptions. The IVF group had higher rates of prematurity (27.8% vs 10.8%, p<0.001), multiple conceptions (37.9% vs 7.4%, p<0.001) and older maternal age (35 vs 30 years, p<0.001). Prematurity in the IVF group had an increased rate of respiratory distress (18.9% vs 12.6%, p=0.05), higher NICU admission rates (13.6% vs 3.2%, p<0.001) and longer hospital stays. Conclusion IVF pregnancies had higher risks of prematurity and respiratory distress, necessitating personalised antenatal care and close monitoring to optimise neonatal outcomes. © Author(s) (or their employer(s)) 2025. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ Group.