Pain assessment in patients with temporomandibular joint (TMJ) disorders during physiotherapy is a challenging yet desired task. Our study addresses two issues. First, we compare the pain perception in patients with TMJ disorders and a control group. The hand dynamometer is verified as an alternate pain self-report device in the second stage. For the dynamometer validation, we employed a cuff-pressure test to induce pain of various intensities. In the second stage, physiological signals (electrodermal activity and blood volume pulse) have been acquired during the physiotherapy in a control group and patients suffering from TMJ disorder. The linear mixed-effects modeling is carried out to find differences in pain and no pain states, considering subjects’ health condition. The main result of the present pilot study is that physiological reactions to painful physiotherapy do not differ between patients with chronic pain and the control group. This finding concludes that studies on TMJ disorder procedures may also be performed on healthy subjects.