An increased incidence of temporomandibular disorders (TMD) among patients with sleep apnea (SA) has been reported. However, the association between TMD and SA has not been demonstrated in a large-scale study. This population-based cohort study with the Taiwan National Health Insurance (NHI) Research Database aimed to understand the association between SA and TMD. We identified adult patients with suspected SA (identified with diagnostic codes) and excluded those diagnosed with TMD prior to SA. Patients with SA diagnosis after polysomnography were also identified as probable SA patients. The index dates were the dates of their initial SA diagnosis. Ten control subjects were matched, by age and sex, to each SA patient, and were assigned the same index dates as the SA patients. In total, 10,408 suspected SA patients (including 4105 probable SA patients) matched to 104,080 control subjects (including 41,050 subjects matched to the probable SA patients) in this study. The TMD incidence rate was significantly higher in the SA patients than in the control subjects (2.8 vs. 1.0 per thousand-patient-year in probable SA patients vs. the corresponding control subjects, with an adjusted incidence rate ratio [95% confidence interval] = 2.5 [2.3–2.7], p < 0.0001). SA patients significantly showed a higher cumulative incidence of TMD than the corresponding control subjects (p < 0.0001). Multivariable Cox regression analysis revealed SA as an independent risk factor for the development of TMD (adjusted hazard ratio = 2.5 [1.7–3.7], p < 0.0001). In summary, this study confirmed an increased TMD incidence in the SA patients. While treating TMD patients, dentists should pay careful attention to the potential underlying SA.