Simple SummaryStressful events can trigger body temperature variations in mammals. The most commonly used methods for measuring temperature in laboratory mice are stressful and invasive in nature, and can themselves cause stress-induced hyperthermia (SIH). This raises concerns regarding both animal welfare and research output. Infrared thermography (IRT) offers a non-invasive alternative, if proven to accurately identify SIH. We exposed mice to mild handling-induced stress, by either tail-picking or the reportedly less-impactful tunnel-handling technique. Temperature was measured by reading microchip devices (PIT-tags) implanted subcutaneously (Tsc), and by a thermal camera to measure mean body surface temperature (Tbody) and mean tail surface temperature (Ttail). As expected, during acute stress exposure, both Tsc and Tbody increased, while Ttail decreased. No differences in stress-induced hyperthermia were found between the two handling techniques. This suggests that such differences may not be detectable in the context of co-occurring stressful events, such as opening of the cage lid, exposure to light, or presence of the handler. Within the same cage, animals handled last consistently showed higher body temperatures than those handled first, raising the issue of minding the order by which animals are tested. Our results suggest IRT offers a reliable non-invasive method for assessing SIH in laboratory rodents.Stress-induced hyperthermia (SIH) is a physiological response to acute stressors in mammals, shown as an increase in core body temperature, with redirection of blood flow from the periphery to vital organs. Typical temperature assessment methods for rodents are invasive and can themselves elicit SIH, affecting the readout. Infrared thermography (IRT) is a promising non-invasive alternative, if shown to accurately identify and quantify SIH. We used in-house developed software ThermoLabAnimal 2.0 to automatically detect and segment different body regions, to assess mean body (Tbody) and mean tail (Ttail) surface temperatures by IRT, along with temperature (Tsc) assessed by reading of subcutaneously implanted PIT-tags, during handling-induced stress of pair-housed C57BL/6J and BALB/cByJ mice of both sexes (N = 68). SIH was assessed during 10 days of daily handling (DH) performed twice per day, weekly voluntary interaction tests (VIT) and an elevated plus maze (EPM) at the end. To assess the discrimination value of IRT, we compared SIH between tail-picked and tunnel-handled animals, and between mice receiving an anxiolytic drug or vehicle prior to the EPM. During a 30 to 60 second stress exposure, Tsc and Tbody increased significantly (p < 0.001), while Ttail (p < 0.01) decreased. We did not find handling-related differences. Within each cage, mice tested last consistently showed significantly higher (p < 0.001) Tsc and Tbody and lower (p < 0.001) Ttail than mice tested first, possibly due to higher anticipatory stress in the latter. Diazepam-treated mice showed lower Tbody and Tsc, consistent with reduced anxiety. In conclusion, our results suggest that IRT can identify and quantify stress in mice, either as a stand-alone parameter or complementary to other methods.