Background Neonates are the most vulnerable population in terms of temperature control. In general, neonates are not able to protect themselves against fluctuations in ambient temperature. We aimed to compare the effect of the prone and supine positions on temperature of premature neonates. Materials and Methods: In this crossover clinical trial, a total of 22 premature neonates between 32-36 weeks of gestation admitted to the Neonatal Intensive Care Unit of Amir Kabir Hospital, Arak, Iran, were selected through purposive sampling technique, and were randomly assigned into groups 1 and 2. Newborns in group 1 were first placed in a prone position (i.e., the first period for 3 hours), and then in a supine position (i.e., the second period for an additional 3 hours). The reverse procedure was applied to the intervention group 2. A trained nurse measured body temperature every minute for three hours with a digital thermometer. Results: Mean age of newborns was 10.38±9.69 days and mean birth weight was 2297.72±693.75 g. The mean temperature at various times in the prone position was significantly higher than the prone position (p <0.05). The mean of body temperature at 1st, 2nd and 3rd hours in the prone position was 36.66 (±0.30), 36.57 (±0.29), and 36.88 (±0.35) and in supine position was 37.18 (±0.09), 37.16 (±0.16), and 37.17 (±0.17), respectively and in all three times, the temperature difference between the two positions was statistically significant (p <0.01). Conclusion Based on the results, placing of premature neonates, admitted to the NICU, in the prone position reduced the body temperature of those with fever or hyperthermia in a non-invasive and non-pharmacological manner and minimized their thermal fluctuations.