The purpose of this prospective case control study is to describe in growing patients with mandibular hypoplasia, treatment outcomes following functional therapy in terms of volumetric changes in nasopharynx and oropharynx, that is, upper and lower pharynx. We recruited 60 study participants aged between 8 and 12 years having mandibular Class II malocclusion and a reduced upper airway (UA) size, as determined by McNamara cephalometric analyses. Forty patients received Twin Block treatment, whereas the remaining 20 patients did not receive treatment, thus constituting the control group. The control group included patients who did not start treatment after their first visit but returned for a consultation one or 2 years later. All patients underwent an initial teleradiography examination of the skull and a final teleradiography examination to measure changes using McNamara cephalometric analysis of the UA. Pretreatment and posttreatment changes were assessed using Student's t test for independent samples with a significance level of 0.05. Both anatomical structures analyzed—the upper pharynx (nasopharynx) and lower pharynx (oropharynx)—showed significant increases after treatment regardless of whether the patients were boys or girls. The controls showed a decrease in UA size on average after approximately 2 years of growth. A clear relationship exists between the mandibular advancement achieved with TB treatment and an increased UA size. Therefore, the appliance is considered suitable for improving the respiratory quality of growing patients with a decreased UA size.