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This study evaluates masticatory efficiency in orthodontic patients with craniofacial disorders compared to controls without, considering the effect of an orthodontic appliance and malocclusion. A total of 119 participants (7–21 years), divided into a craniofacial disorder and control group (n = 42 and n = 77; mean age 13.5 ± 5.2 and 14.2 ± 3.3 years) were included. Masticatory efficiency was evaluated using a standard food model test, where masticated test food bodies were analyzed, and parameters like particle number (n) and area (mm2) were recorded. This study newly introduced the masticatory efficiency index (MEI), which encompasses the above terms (number and area), with a high MEI being an indicator of high masticatory ability. Younger orthodontic patients with a craniofacial disorder had a significantly decreased MEI (0.50 ± 0.25 n/mm2) compared to patients without (1.10 ± 0.48 n/mm2; p = 0.02). The presence of a crossbite significantly decreased masticatory efficiency, particularly in craniofacial disorder patients (0.69 ± 1.44 n/mm2) versus controls (0.89 ± 1.00 n/mm2, p = 0.04). As treatment progressed with age and fixed appliances, mastication group differences became non-significant, suggesting that patients with a craniofacial disorder were catching up to healthy controls in the rehabilitation of their masticatory function. Considering an early diagnosis of malocclusion during orthodontic therapy in combination with speech therapy can avoid negative malocclusion effects with growth, caused by muscle imbalances.