Introduction: Cleft lip and palate is among the most common congenital craniofacial malformations and is associated with functional, esthetic, and psychosocial morbidity. Its origin is multifactorial and involves genetic, environmental, and sociodemographic factors. These alterations can affect maxillofacial growth and temporomandibular joint function.

Aim: To perform a comprehensive three-dimensional Cone Beam computed Tomography-based evaluation of condylar morphology and TMJ joint space characteristics in patients with complete unilateral cleft lip and palate during the growth phase.

Materials and Methods: A cross-sectional observational study was conducted among 15 patients with unilateral cleft lip and palate aged 12–18 years. CBCT images were analyzed using OnDemand3D software following previously described criteria for the three-dimensional evaluation of joint space and condylar morphology.

Results: There were no statistically significant differences between the affected side and the normal side of the TMJ in most measurements, except for the roof of the glenoid fossa. Additionally, 73% of the patients presented with a more anterior condylar position on the affected side, and 86% showed condylar morphological alterations characterized by greater width and shorter height.

Conclusions: CBCT plays a critical role in detecting dimensional changes in the TMJ in unilateral cleft lip and palate, offering superior diagnostic precision and improving clinical decision-making regarding significant condylar asymmetry.