Hypothermia, a factor associated with neonatal mortality, can occur immediately after birth as a protective mechanism to prevent hypoxic damage in neonates, or to reduce the metabolic rate to improve the chances of survival in the first hours of life. The heat interchange through the superficial temperature of animals can be evaluated with infrared thermography (IRT). However, to date, there is no information on thermal windows in puppies. This study aimed to evaluate, with the use of IRT, the microcirculatory alterations in 8 different thermal windows identified at 7 different times in 289 newborn puppies assigned to different groups. Three thermograms were taken from four zones of each puppy: the facial, frontal, right lateral, and left lateral regions. Newborn puppies were grouped in 4 quartiles according to their weight: Q1 (126–226 g) n = 73, Q2 (227–330 g) n = 72, Q3 (331–387 g) n = 74, and Q4 (388–452 g) n = 70. A total of 8 thermal windows were considered at 7 evaluation times from Wet at birth until 24 h after birth (AB). Two-way mixed ANOVA within and between subjects’ design for each thermal window (eight models) was performed. Results revealed a positive correlation between the puppy’s weight and its ability to achieve thermostability in all the evaluated thermal windows. Statistically significant differences (p < 0.0001) between the 4 quartiles (Q1, Q2, Q3, and Q4) were found. The lowest temperatures were recorded when the pups were still wet and the highest at 24 h AB. Thermal windows with the highest temperatures were abdominal (34.234 ± 0.056 °C), thoracic (33.705 ± 0.049 °C), nasal (30.671 ± 0.110 °C), and upper left palpebral (34.066 ± 0.052 °C), while the lowest were thoracic limb brachial biceps (27.534 ± 0.051 °C), thoracic limb elbow (27.141 ± 0.049 °C), thoracic limb metacarpal (27.024 ± 0.062 °C), and femoral pelvic limb (27.654 ± 0.055 °C). Assessing the thermal response in newborn puppies can help identify drastic temperature reductions or deficient thermoregulatory compensation during the first hours of life, preventing the consequences of hypothermia.