The purpose of this study was to assess the effectiveness of the expander with differential opening (EDO) with alternate rapid maxillary expansion and contraction (Alt-RAMEC), and Facemask Protraction in patients with cleft lip and palate using cone beam computed tomography (CBCT) records. Material and methods: Eight cleft lip and palate patients, ages 8 to 12, were selected. All patients had maxillary permanent first molars and displayed a constricted maxillary arch. Primary lip adhesion and palatal closure were done in early childhood. All patients treated with the Alt-RAMEC protocol used EDO and a protraction facemask. CBCT scans were taken both before and six months after treatment. Maxillary transverse dimensions were measured, including the nasal cavity width, maxillary width, alveolar crest width, arch width, inclination of the molar teeth, alveolar width, alveolar crest level, and buccal and palatal bone plate thickness. A paired-sample t-test for significance was used when comparing related samples. The Pearson's correlation coefficient (r) test was used to assess the degree of association between two sets of variables. Results: All maxillary transverse measurements increased significantly at the molar and premolar regions (p<0.05). Alveolar crest level and buccal bone plate thickness were slightly decreased (0.57mm) and 0.5 mm, respectively (p<0.05). The molar teeth showed a significant increase in buccal inclination (6.36°) (P<0.001). Forward movement of the maxilla was seen in the lateral cephalometric extract from CBCT. Conclusion: Significant maxillary expansion and advancement were achieved while using the EDO with Alt-RAMEC and facemask protraction, while there was a slight decrease in buccal bone thickness and height and a significant increase in buccal molar inclination. Registration: This trial was registered at ClinicalTrials.gov with the identifier NCT04970095, and the date of registration was July 16, 2021. Clinical Relevance: This innovative treatment approach corrects anterior and posterior crossbite in patients with cleft lip and palate who have dentoskeletal anomalies.