Temporomandibular disorders (TMDs) and cervical spine problems are a growing public health issue, as they increase the risk of disability in people with hypermobility joint syndrome (HJS). The present study aimed to assess the prevalence of TMD symptoms, and cervical spine and TMJ disability in HJS patients. A survey was conducted among physical therapy students (mean age: 21 years). The study comprised 2 stages. The 1st one was HJS assessment (the Beighton scale and the Brighton criteria). Based on the assessment, 56 HJS subjects were enrolled for the study. The control group (CG) consisted of 60 HJS-free subjects, according to the aforementioned criteria. The 2nd stage of the study involved conducting a self-administered questionnaire on the prevalence of TMD symptoms. Both the TMD disability questionnaire (TMD-Q) and the neck disability index (NDI) scores were recorded. Pain intensity was assessed using the numeric rating scale (NRS). The HJS group showed higher NRS scores (p < 0.001). Headache, neck and shoulder girdle pain, and temporomandibular joint (TMJ) pain were found to be more severe in almost each patient from the HJS group as compared to CG. Those individuals had a greater degree of disability on the TMD-Q and the NDI scales (p < 0.001). The HJS group showed significant positive correlations between the TMD-Q and NDI scores (p = 0.0035), and between the TMD-Q and TMJ symptom questionnaire scores (p = 0.0047). A significant positive correlation between the NDI and TMJ symptom questionnaire scores was found both in the HJS group (p < 0.001) and CG (p < 0.001). The HJS bearers tended to obtain higher TMJ and cervical spine disability scores, at the same time reporting increased headache, neck and shoulder girdle pain, and TMJ pain intensity. Therefore TMJs should be carefully examined for possible signs of dysfunction in HJS subjects prior to dental or prosthetic treatment. According to our data, TMJ and cervical spine disability assessment should be included as a routine practice in the case of HJS patients, who should remain under the long-term care of a multidisciplinary team of doctors and therapists.