The aim of the present study was to examine pain threshold and pain recovery in patients with burning mouth syndrome (BMS) and matched no-pain controls. Twenty female patients diagnosed with BMS without organic gross changes were enrolled in the study. Twenty control subjects were chosen from age-matched healthy female volunteers. We compared the thermal pain threshold using heat beam dolorimeter on the finger and tongue between patients and controls. Warm (at 50°C for 5 s), cold (at 0°C for 30 s) and mechanical (stimulation by electric tooth brush for 15 s) stimulation was applied to the tongue for both groups. Participants were asked to rate the subjective pain using a visual analogue scale (VAS). Although there was no significant differences between patients and controls in terms of the threshold on the finger, the threshold on the tongue was significantly higher in patients than in controls. We suggest there were peripheral dysfunction at the tongue, and/or central dysfunction in patients with BMS. Among the three types of stimulation, the patients perceived significantly the highest pain from the mechanical stimulation for the first 5 min after the stimulation. Furthermore, when patients with BMS perceived some pain, they continued to complain of the pain longer and more intricately than the controls. This indicates that the pain of the patients is strongly affected not only at a sensory component but also at an affective/motivational component than the controls. However, we should be cautious of simply advancing psychogenic theory in this etiology.