•Alternate rapid maxillary expansion and constriction (Alt-RAMEC) was studied. •Results were compared with facemask therapy and rapid maxillary expansion. •Alt-RAMEC was performed simultaneously with maxillary protraction. •Alt-RAMEC along with facemask therapy produced more favorable skeletal effects. •No short-term abnormal dental, periodontal, or craniofacial changes were observed. Introduction This study aimed to investigate the relative efficacy of maxillary protraction combined with a modified alternate rapid maxillary expansion and constriction (Alt-RAMEC) protocol compared with conventional protocols in the early orthopedic treatment of skeletal Class III malocclusion. Methods A sample of 39 patients was divided into 3 groups on the basis of different interventions. Conventional facemask (FM) with splint-type intraoral devices was performed in the FM group (7 males and 5 females; mean age, 9.53 ± 1.37 years). Maxillary expansion with an activation rate of 0.5 mm/d (twice a day) followed by FM therapy was applied in the rapid maxillary expansion group (RME/FM) (6 males and 6 females; mean age, 9.31 ± 1.60 years). In the Alt-RAMEC/FM group (7 males and 8 females; mean age, 10.01 ± 1.31 years), Alt-RAMEC was started simultaneously and throughout the entire course of maxillary protraction, with repetitive alternations between activation and deactivation of expanders (0.5 mm/d for 7 days). The patients in all groups were instructed to wear FMs for a minimum of 12 h/d. Pretreatment and posttreatment lateral cephalograms were all traced and measured. Results The Alt-RAMEC group showed statistically more significant maxillary advancement than other groups (A-VRP, 3.87 mm vs 3.04 mm [RME/FM], vs 2.04 mm [FM]; P <0.05). Analysis of variance did not reveal significant intergroup differences in palatal plane angulation changes (P >0.05). No pronounced mandibular clockwise rotations were noted in the Alt-RAMEC/FM group with distinct intergroup differences (P <0.05). There were more skeletal effects (88.7%) during overjet correction in the Alt-RAMEC/FM protocol. Conclusions A combination of the modified Alt-RAMEC protocol with FM revealed more favorable skeletal effects compared with FM and RME/FM protocols in treating prepubertal patients with maxillary deficiency.