Introduction: This research aimed to compare treatment effects of functional appliances between children with and without morphologic deviations in the upper spine and analyze associations between Atlas dimensions and the short- and long-term treatment effects. Methods: Sixty-eight prepubertal or pubertal children (35 boys and 33 girls; mean age, 11.47 ± 1.39 years) treated with Class II functional appliances were included. Lateral cephalograms were taken at pretreatment (T1), postfunctional appliance treatment (T2), and after retention at postpuberty (T3). Upper spine morphology and Atlas dimensions were evaluated at T1. T1-T2 and T1-T3 lateral cephalograms were superimposed using a structural method. Changes in the jaws were compared with multiple linear regression analysis between children with and without deviations in the upper spine. Associations between the changes and Atlas dimensions were analyzed by partial correlation. Results: Children with morphologic deviations in the upper spine showed significantly more backward rotation of the mandible (P <0.01) and increased inclination of the jaws (P <0.05, P <0.01) from T1-T2 and significantly smaller condylar growth (P <0.01) from T1-T3 compared with children without the deviations. Atlas height was significantly associated with vertical and rotational changes in the mandible (P <0.01) from T1-T2 and condylar growth (P <0.05) from T1-T2 and T1-T3. Conclusions: Morphologic deviations in the upper spine and low Atlas height were significantly associated with smaller condylar growth induced by functional appliances in the long term. Upper spine morphology and the Atlas dimension may be valuable in phenotypic differentiation in children with Class II malocclusion for optimal treatment outcome.