Occlusal splints are used as a non-invasive treatment for patients diagnosed with temporomandibular disorders (TMD). Another non-invasive treatment option for TMD patients is kinesiotherapy, which may be used alone or in conjunction with occlusal splint therapy. The aim of this study was to evaluate the changes in the intra-articular spaces of the temporomandibular joint (TMJ) after occlusal splint therapy combined with cranio-temporomandibular kinesiotherapy in TMD patients. Twenty-four patients (N = 24) diagnosed with TMD according to Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) were included. Cone beam computed tomography (CBCT) images were taken before and after treatment. The anterior, superior, posterior, and medial joint spaces were measured on the CBCT images, and the condylar ratio was calculated using Pullinger and Hollender’s formula. Additionally, the thickness of the glenoid fossa (GFT), condylar medio-lateral widths (MLW), and condylar height (HCo) were measured. The condylar ratio was significantly higher after treatment (p = 0.049). The changes in dimensions of the anterior, superior, posterior and medial joint spaces were not statistically significant after treatment. No statistically significant differences were found in the dimensions of the GFT, MLW, and HCo post treatment. The condylar position did not shift anteriorly in a statistically significant way after occlusal splint therapy combined with cranio-temporomandibular kinesiotherapy in TMD patients.