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Temporomandibular disorders (TMDs) are frequently associated with psychological stress. Their prevalence appears particularly high in populations exposed to substantial stress, such as students during examination periods. While subjective assessments have linked TMDs to psychological stress, physiological evidence remains limited. Heart rate variability (HRV) is an established biomarker of autonomic regulation and stress reactivity and may therefore be useful for characterizing stress responses in individuals with TMD symptoms. This study investigated stress reactivity in students with and without TMD symptoms using HRV as a physiological marker within a standardized stress protocol. A total of 138 healthy students (aged 23–36 years) were recruited. TMD symptoms were assessed using a standardized protocol based on bruxism guidelines, focusing on palpation-evoked pain and limitations in mandibular range of motion. Psychological stress and depressive symptoms were assessed using the Perceived Stress Scale (PSS) and the Beck Depression Inventory-II (BDI-II), respectively. Acute stress was induced using the Trier Social Stress Test (TSST). HRV was recorded at baseline, during the pre-stress phase, and during stress exposure. RR intervals were analyzed using Kubios software, with the root mean square of successive differences (RMSSD) as the primary HRV parameter. Statistical analyses used linear mixed-effects models adjusted for potential confounders, including age, sex, and baseline stress levels. TMD symptoms, particularly palpation-evoked pain, were significantly associated with psychological stress measures (p < 0.005). Students with TMD symptoms also showed higher depressive symptom scores (p < 0.002). Due to participant dropout, statistical power for HRV analyses was limited; however, effect estimates suggested a trend toward prolonged autonomic dysregulation in students reporting TMD-related pain. The findings provide preliminary physiological evidence linking TMD symptoms to psychological stress and indicate altered autonomic stress responses in students with TMD pain. Early symptom recognition and the integration of stress management strategies may be beneficial components of TMD care. Future research should incorporate additional biomarkers (e.g., cortisol) and use larger longitudinal designs to improve clinical applicability.