Understanding animal emotions has become a key point for improving animal welfare worldwide. The aim of this study was to investigate the influence of an emotional context in the eye temperature of dogs, measured via infrared thermal imaging (IRT), in a separation-reunion experiment. We tested 61 adult pet dogs, with a straightforward experiment composed of three phases of five minutes each: baseline, separation and reunion. Due to its less variability in temperature, we opted for the eye area as the area of interest in the IRT analysis.  Results showed that temperature significantly differs across phases, with the baseline temperature significantly higher than separation and reunion. Temperature continuously decreased throughout the experiment in both, test and control condition. Descriptive physiological results showed temperature fluctuations of over one degree within a minute and throughout the experiment. In order to verify the validity of the obtained results and the utilised thermo camera, we conducted five additional experiments with different subjects. The results of the additional experiments showed temperature fluctuations, indicating the presence of a malfunction in the equipment. The degree of temperature fluctuations obtained from the additional results were different depending on the subject, and were minimal when testing an handle door or an electric device, suggesting that multiple factors influence IRT measurements. Therefore, assessing the emotional status in dogs via IRT requires additional investigations, proper validation of the equipment and a straightforward experiment.