The aim of this study was to evaluate changes in the pharyngeal airway in growing children and adolescents and to compare these with a group of children who received activator-headgear Class II treatment. The sample consisted of 64 children (32 males and 32 females), 32 had a combined activator-headgear appliance for at least 9 months (study group) followed by fixed appliance therapy in most patients, while the other half received only minor orthodontic treatment (control group). Lateral cephalograms before treatment (T1, mean age 10.4 years), at the end of active treatment (T2, mean age 14.5 years), and at the long-term follow-up (T3, mean age 22.1 years) were traced and digitized. To reveal the influence of somatic growth, body height measurements were also taken into consideration. A two-sample t-test was applied in order to determine differences between the groups. At T1, the study group had a smaller pharynx length (P = 0.030) and a greater ANB angle (P < 0.001) than the controls. The pharyngeal area and the smallest distance between the tongue and the posterior pharyngeal wall also tended to be smaller in the study group. During treatment (T1-T2), significant growth differences between the two groups were present: the study group had a greater reduction in ANB (P < 0.001) and showed a greater increase in pharyngeal area (P = 0.007), pharyngeal length (P < 0.001) and the smallest distance between the tongue and the posterior pharyngeal wall (P = 0.038). At T2, the values for the study group were similar to those of the control group and remained stable throughout the post-treatment interval (T2-T3). Activator-headgear therapy has the potential to increase pharyngeal airway dimensions, such as the smallest distance between the tongue and the posterior pharyngeal wall or the pharyngeal area. Importantly, this increase seems to be maintained long term, up to 22 years on average in the present study. This benefit may result in a reduced risk of developing long-term impaired respiratory function.