Heat stress (HS) exerts detrimental effects on animal production, with lactating sows being particularly vulnerable. Understanding the mechanisms involved in HS response could aid in developing effective strategies against the negative impacts on livestock. Recent genome wide association studies identified two core circadian clock genes as potential candidates in mediating HS response. The study aimed to investigate how cooling lactating sows under natural heat stress conditions impacted circadian patterns of respiration rate (RR), rectal temperature (RT), behavior, salivary melatonin and cortisol levels, and diurnal patterns of cytokines in saliva. Mixed parity lactating sows were assigned to one of two treatment groups: electronic cooling pad (C; n = 9) and heat-stressed (H; n = 9). The experiment spanned two 48 h periods of elevated ambient temperatures due to summer heat wave. In the first 48 h period, RR was recorded every 30 min, RT every 60 min, and behaviors (eating, standing, sitting, laying, sleeping, drinking, and nursing) every 5 min. In the second 48 h period, saliva samples were collected every 4 h. Cooling reduced RR and RT and altered circadian patterns (P < 0.05). Cooling did not affect amount of time engaged in any behavior over the 48 h period (P > 0.05), however, daily patterns of eating, standing and laying differed between the treatments (P < 0.05), with altered eating behavior related to RT increment in H sows (P < 0.05). Cooling increased and altered the circadian pattern of salivary melatonin (P < 0.05). Cooling also influenced the diurnal pattern of saliva cytokines. Cooling had no impact on saliva cortisol levels. In conclusion, cooling HS sows impacted circadian rhythms of physiology and behavior, supporting the need for further research to understand if circadian disruption underlies decreased production efficiency of HS animals.