Transport is a stressor that can cause physiological and metabolic imbalances in livestock, resulting in stress-induced hyperthermia. In water buffaloes, studies regarding the thermal state of animals during mobilization are scarce. Therefore, this study aimed to compare the thermal response of 1516 water buffaloes using infrared thermography (IRT) during 15 short trips (783 animals, 60,291 records, average duration = 50.33 min ± 5.48 min) and 14 long trips (733 animals, 56,441 records, average duration = 13.31 h ± 47.32 min). The surface temperature was assessed in 11 regions (periocular, lacrimal caruncle, nasal, lower eyelid, auricular, frontal-parietal, pelvic limb, torso, abdominal, lumbar, and thoracic) during seven phases from pasture to post-transport. It was found that the surface temperature of the periocular, lacrimal caruncle, nasal, auricular, frontal-parietal, pelvic limb, torso, abdominal, lumbar, and thoracic regions was significantly higher during SJs (+3 °C) when compared to LJs (p < 0.0001). In particular, the frontal-parietal region had a significant increase of 10 °C during the post-transport phase (p < 0.0001) in both groups, recording the highest temperatures during this phase. Likewise, a strong positive significant correlation between the different regions was found (r = 0.90, p < 0.0001). It is worth mentioning that the herding, loading, pre-, and post-transport phases were the ones where the greatest thermal response was recorded, possibly due to the influence of human interaction. Finally, a strong positive correlation (r above 0.9, p > 0.001) between the periocular, lacrimal caruncle, pinna, and pelvic limb was found. According to the results, SJ could be considered a stressful event that hinders thermal generation, contrarily to LJ.