Background: The first few minutes after birth are the most dangerous for the survival of an infant. Babies in neonatal intensive care units are either under heated or overheated, and hypothermic infants remain hypothermic or develop a fever. As a result, special attention must be paid to monitoring and maintaining the time of recovery from hypothermia states. Despite numerous studies, only a few have examined the transition from neonatal hypothermia and associated risk factors in depth. Method: A retrospective observational study was conducted to track axillary temperatures taken at the time of neonatal intensive care unit admission, which were then tracked every 30 minutes until the newborn's temperature stabilized. All hypothermic neonates admitted to the neonatal intensive care unit between January 2018 and December 2020 was included in the study. Temperature data were available at birth and within the first three hours of admission for 391 eligible hypothermic neonates. The effect of factors on the transition rate in different states of hypothermia was estimated using a multi-state Markov model. Result: The likelihood of progressing from mild to severe hypothermia was 5%, while the likelihood of progressing to normal was 34%. The average time spent in a severe hypothermia state was 48, 35, and 24 minutes for three different levels of birth weight, and 53, 41, and 31 minutes for low, moderate, and normal Apgar scores, respectively. Furthermore, the mean sojourn time in a severe hypothermia state was 48, 39, and 31 minutes for three different levels of high, normal, and low pulse rate, respectively. Conclusion: For hypothermic survivors within the first three hours of life, very low birth weight, low Apgar, and high pulse rate had the strongest association with hypothermia and took the longest time to improve/recover. As a result, there is an urgent need to train all levels of staff dealing with maintaining the time of recovery from neonatal hypothermia.