This prospective controlled trial aimed to evaluate the skeletal effect of 3.5-years bone anchored maxillary protraction (BAMP) in growing cleft subjects with a Class III malocclusion. Subjects and Method: Nineteen cleft patients (11.4 ± 0.7-years) were included from whom cone beam computed tomography (CBCT) scans were taken before the start of BAMP (T0), 1.5-years after (T1) and 3.5 y after (T2). Seventeen age- and malocclusion-matched, untreated cleft subjects with cephalograms available at T0 and T2 served as the control group. Three dimensional skeletal changes were measured qualitatively and quantitatively on CBCT scans. Two dimensional measurements were made on cephalograms. Results: Significant positive effects have been observed on the zygomaticomaxillary complex. Specifically, the A-point showed a displacement of 2.7 mm ± 0.9 mm from T0 to T2 (p < 0.05). A displacement of 3.8 mm ± 1.2 mm was observed in the zygoma regions (p < 0.05). On the cephalograms significant differences at T2 were observed between the BAMP and the control subjects in Wits, gonial angle, and overjet (p < 0.05), all in favor of the treatment of Class III malocclusion. The changes taking place in the two consecutive periods (ΔT1-T0, ΔT2-T1) did not differ, indicating that not only were the positive results from the first 1.5-years maintained, but continuous orthopedic effects were also achieved in the following 2-years. Conclusions: In conclusion, findings from the present prospective study with a 3.5-years follow-up provide the first evidence to support BAMP as an effective and reliable treatment option for growing cleft subjects with mild to moderate Class III malocclusion up to 15-years old.