Neonatal transport is a highly specialized medical service that shifts critically ill neonates between hospitals for on-going care. In other words, it is an extension of the Neonatal Intensive Care Unit (NICU), which provides intensive care to critical ill neonates during transport. Furthermore, pain assessment and management is a crucial element during neonatal transport. However despite significant advances over the last 20 years in relation to our understanding of pain mechanisms in the neonates, the immediate long and short term consequences of neonatal pain along with proliferation of pain assessment measures, there continues to be reports of neonates in a variety of settings suffering needlessly from acute, prolonged, persistent and chronic pain. The central focus of the present review article is to put light on the existing challenges accompanying neonatal pain assessment during transport.