Some studies on epilepsy have shown that seizures might change the body temperature of a patient. Furthermore, other works have shown that kainic acid, a drug used to study seizures, modify body temperature of a laboratory rat. Thus, thermographic cameras may have an important role in investigating seizures. In this paper, we present the methods we have developed to measure the temperature of a moving rat subject to seizure using a thermographic camera and image processing. To accurately measure the body temperature, a particle filter tracker has been developed and tested along with an experimental methodology. The obtained measures are compared with a ground truth. The methods are tested on a 2-hour video and it is shown that our method achieves the promising results.